bluuebunny/crossref_metadata_2025 huggingface dataset:
Trying to change a gender-marked language
Authors: Muchnik Malka
Published: November 2016

Classical and Modern Hebrew are gender-marked in all morphological forms,
and the rules of Hebrew syntax require gender agreement. Consequently, it is
next to impossible to find a sentence without gender determination. Masculine
content words are unmarked, while feminine words are derived from them.
Masculine forms are also used generically, making them more visible than the
feminine. Feminine function words, mainly pronouns, were used in classical
periods for the masculine as well, leaving less specific features for the feminine.
We could expect that feminist speakers would try to change this practice in
Modern Hebrew despite the rigid linguistic structure. However, there have been
only a few gender changes, mostly in one direction: using masculine, but not
feminine forms, for both sexes. This article provides examples of this sociolinguistic
change and explains why it has taken this direction.
A poststructuralist approach to structural gender linguistics
Authors: Motschenbacher Heiko
Published: November 2016

This article attempts to counter the contemporary marginalisation of
structural gender linguistics within the field of language and gender. It argues
that, in order to make structural gender linguistics compatible with recent
developments in the field, it is necessary to initiate a conceptual shift from treating
language structures as stable parts of a language system to viewing them as
unstable and ever-changing in linguistic performance. This theoretical move
towards a poststructuralist approach to structural gender linguistics also
has methodological consequences. Its central aim is the de-essentialisation of
gendered language structures by documenting their heterogeneity, instability and
incoherence. This can be achieved in three major ways: cross-linguistic comparison,
historical linguistic description and analysis of the usage patterns of particular
forms. The three methods are illustrated using language material from English,
German and Croatian.
A hermeneutical approach to gender linguistic materiality
Authors: Abbou Julie , Tse Angela
Published: November 2016

While most Cantonese grammar textbooks draw on the assumption that
gender is absent in this language, the fact, however, remains that the masculine/
feminine relationship – and its consequential social assignation – is indeed
expressed in it. This study explores how and where gender is indexed
in the linguistic materiality of Cantonese. To serve such purpose, an interdisciplinary
framework is built at the crossroads of linguistics and gender studies
towards a hermeneutical re-definition of gender as a semiotic form structuring
power relationships. This framework leads to an investigation of gender from
a contrastive perspective. A corpus of translated sentences from English to
Cantonese displays significant “gender shifts” in the interlingual space, which
makes gender marking in Cantonese visible in different linguistic levels.
The representation of gender in Bajjika grammar and discourse
Authors: Kumar Kashyap Abhishek
Published: November 2016

In this article I present a description of grammatical gender in Bajjika, a
minority language of the Eastern Indo-Aryan family spoken in a small region
in the northern part of the north Indian state of Bihar. Grammatical gender in
Bajjika is expressed in the nominal forms, definitive particles, and verbal agreement.
Although the morphology of Bajjika verb-agreement is one of the most
elaborate in Indo-Aryan languages, the formalization of gender in the verbal
morphology is very simple; the gender of only the second person honorific
and the third person honorific referents in the subject function is encoded. The
definitive particle receives gender marking when it is added to an adjective. In
this article, I identify and describe different areas of Bajjika grammar where
gender is encoded. Based on the analyses of excerpts from natural discourse, I
also observe an interesting tendency in terms of (written and spoken) modebased
neutralization of gender in Bajjika discourse. While the masculine and
feminine genders of the second and third person “honorific” referents are
consistently encoded in the verb-agreement in the spoken mode, in the written
mode it is neutralized. We may then witness a potential neutralization of gender
in terms of a diachronic change in the Bajjika grammar.
Lakota men’s and women’s speech
Authors: Nelson Jessica Fae
Published: November 2016

Although most words in Lakota [a Siouan language] do not indicate gender,
some can be used by speakers to mark their own gender. Recently perceptions
of the use of gender-indexing words have shifted, altering the ranges of sociolinguistic
expression available to speakers. Scholars have argued that speakers are
able to take advantage of shared understandings about norms for gender-indexing
words in order to construct alternative social meanings (see Trechter 1995;
Agha 2005). I compare metapragmatic discourse about Lakota gender-indexing
assertion enclitics from two different time periods in order to analyze changes
in perception about this kind of gendering speech. I argue that in the current
context of Lakota language shift and revitalization, metapragmatic discourses
are erasing some of the indirect indexical links of gender-indexing words, and
attributing other meanings that limit the potential that speakers have to use
such words to communicate a broader range of social meanings in Lakota.
“Moldovan” and feminist language politics
Authors: Weirich Anna Christine
Published: November 2016

The notion of “peripheral linguistic market” accounts for linguistic practice common
to a non-dominant group of speakers with endogene rules that are set up
in opposition to the “official linguistic market”, yet dependent on them. Against
this background, the practice of Moldovan / Romanian and antisexist linguistic
practices can be considered as distinct peripheral markets that hardly interact
with each other. Explanations for the absence of antisexist linguistic practices
and research on language and gender in Moldova could start from this hypothesis.
Despite its inflectional complexity and conservative linguistic practices, the
grammatical structure of Romanian/Moldovan offers multiple opportunities for
anti-sexist interventions. However, research has shown that becoming aware of
the multiple dimensions of grammatical gender in Romanian/Moldovan is a challenge,
even for speakers with elaborated registers and metalinguistic knowledge.
Examples of feminization and double gendering strategies developed by participants
in an experimental workshop are presented and discussed in this article.
Eastern boys and girls! Comparative linguistic anthropologies
of lesbian and gay communities, Kuala Lumpur and Sorwool
Authors: Hadzantonis Michael Dimitrios
Published: November 2016

Motivated by social inclusion, lesbian and gay communities have long attempted
to negotiate languages and connected discourses. Social ascriptions act to
oppress these communities, thus grounding Cameron’s (1985) Feminism and
Linguistic theory. This practice of language negotiation significantly intensifies
in regions where religious piety (Hinduism, Christianity, Buddhism, Islam)
interacts with rigid social structure (Confucianism, Interdependency), mediating
social and cultural positioning. Consequently, members of LG communities
build linguistic affordances, thus (re)positioning selves so to negotiate ascribed
identities and marginalizations. Paradoxically, these communities model, or
draw from, discourses and dynamics of those larger sociocultural networks with
which intercommunal boundaries exist, so to contest or alleviate marginalizations,
thus repositioning self and other in sociocultural interstices.
Through a comparative framework, the current study
employs ethnography, as well as conversation and discourse analyses, of LG communities,
to explore ways in which these communities in Kuala Lumpur and Sorwool
(Seoul) develop and employ adroit language practices to struggle within social
spaces, and to contest positivist ascriptions.
Translating for a healthier gaming industry
Authors: Pan Hanting , Zhang Meifang
Published: November 2016

This article conducts a corpus-based critical discourse analysis of keywords and their translations in Macao’s gaming discourse, with an aim to explore the impact of translation on the construction of gaming discourse and the development of the gaming industry in Macao from 1999 to 2011, the first decade following the region’s sovereignty handover. The corpus consists of texts from 2000 to 2011 concerning three public sectors in Macao: local government, academia and the media. The study finds diachronic as well as synchronic changes in the distribution and translation of certain keywords in the corpus. It argues that shifts in the keyword terminology being used, such as from ‘gambling’ to ‘gaming,’ aim at framing the Macao gaming industry in specific social developmental ways. It also argues that translation plays a crucial role in the construction of a new gaming discourse.
Translating time and space in the memorial museum
Authors: Liao Min-Hsiu
Published: November 2016

Translation has long been conceptualized in metaphors of space, whereas its temporal aspect is relatively underexplored. However, recently scholars have argued that translation does not only carryacrossbut also carriesforward, i.e., texts survive through time. The aim of this study is to examine how time and space are manipulated in translation, with a particular focus on how the two dimensions interact with each other. To achieve this aim, a memorial museum has been chosen for investigation. A museum, as a site to display dislocated objects from the past, constructs a unique temporal-spatial dramaturgy. This study argues that shifts of temporal-spatial frames in museum translations have a significant impact on how a nation’s past, present and future are perceived by target readers.
“Should she really be covered by her own subtitle?”
Authors: Fox Wendy
Published: November 2016

This article provides a first concept of typographic identity in film and the impact of audiovisual translation on it. Based on an analysis of 52 films, relevant text elements and their graphical translation strategies in film were identified. Finally, possible shortcomings and challenges such as collisions and the impact on a film’s typographic identity and image composition are discussed as a first basis for further studies
Anthropogenic Impacts Facilitate Native Fish Hybridization in the Bonneville Basin of Western North America
Authors: Bangs Max R. , Douglas Marlis R. , Thompson Paul , Douglas Michael E.
Published: November 2016

Habitat modification and introduced species are impacting native fishes in western North America, a situation now exacerbated by drought and anthropogenic water acquisition. One species of concern, the Bluehead Sucker Catostomus discobolus in the Bonneville basin of Utah, Idaho, and Wyoming, has experienced sharp population declines potentially augmented by hybridization with native Utah Sucker C. ardens. To evaluate this situation, we sequenced three diagnostic nuclear DNA loci and two mitochondrial genes across 81 Bluehead Suckers, 74 of which were collected in a basinwide genetic assessment and 7 from a targeted morphological evaluation. Combined, we detected 14 hybrids from the single site in the Bear River and the three sites in the Weber River that hosts the three largest remaining populations in the basin. All individuals sampled as putative hybrids were confirmed as F1 hybrids, ascertaining efficacy of field‐based morphological identifications. Hybridization may be especially problematic for the numerically reduced Bluehead Sucker because it can further depress recruitment. However, no evidence of post‐F1 backcrosses was found, suggesting in turn that hybrids are not reproducing, although the reasons for this are currently not understood. These results underscore the need to quantify the proportion of Bluehead Sucker recruitment lost to hybridization.

Received January 6, 2016; accepted August 31, 2016 Published online November 28, 2016
Multi-Criteria Decision Analysis for Recreational Trout Fisheries in British Columbia, Canada: A Bayesian Network Implementation
Authors: Varkey Divya A. , McAllister Murdoch K. , Askey Paul J. , Parkinson Eric , Clarke Adrian , Godin Theresa
Published: November 2016

One of the key challenges in recreational fisheries management is to provide a rational basis for decisions in the face of conflicting objectives, such as improving angling opportunities, maintaining satisfaction across a diverse fishing client base, controlling costs, and conserving wild populations. We developed a multi-criteria decision analysis approach for managing recreational trout fisheries (e.g., Rainbow Trout Oncorhynchus mykiss). The approach was implemented in a Bayesian decision network. The decision support tool, called “Stock-Optim,” provides a user-friendly interface for predicting fishery performance from alternate stocking prescriptions. The tool integrates survey information on angler typology and satisfaction with previously developed models for fish biology and fishery dynamics to more fully consider the biological and social outcomes of management decisions. Specifically, the tool evaluated alternative stocking options given three performance criteria: angler effort, angler satisfaction, and the cost of the stocking program. Predicted effort was highest for fish that were released in the size range of 8–20 g and at stocking densities of 200–500 fish/ha. Effort maximization at these rates and sizes is a result of compromise between the conflicting preferences of Rainbow Trout enthusiasts and occasional anglers toward fish size and harvest. Furthermore, lowering the stocking program's costs will lead to lower stocking rates and thereby favor the enthusiasts. Currently, stocking levels in British Columbia are lower than levels that would maximize effort and are most consistent with a policy of maximizing satisfaction for Rainbow Trout enthusiasts and minimizing costs. Stock-Optim will allow managers to compare predicted outcomes from the current and alternative regimes with stated lake-specific or region-specific management objectives and regional averages and thereby more closely meet these objectives in the future. Lastly, the model was validated by comparing predicted effort with observed effort in stocked lakes.

Received February 1, 2016; accepted July 14, 2016 Published online November 28, 2016
Genetic Stock Structure of Anadromous Arctic Char in Canada's Central Arctic: Potential Implications for the Management of Canada's Largest Arctic Char Commercial Fishery
Authors: Harris Les N. , Moore Jean-Sébastien , Bajno Robert , Tallman Ross F.
Published: November 2016

The Arctic Char Salvelinus alpinus is widely considered the most important subsistence fish species in the Canadian Arctic. Throughout the species’ range, commercial fisheries for Arctic Char also exist, the management of which primarily follows river-specific harvest strategies. Such an approach, however, may not be appropriate if the management unit or stock does not accurately reflect a demographically independent population or if mixtures of populations are being harvested. We assayed microsatellite DNA variation among 744 Arctic Char from the Cambridge Bay region, Nunavut, where the largest commercial fishery for the species exists, in order to identify the most appropriate spatial scale at which these stocks should be managed. Our sampling design specifically mirrored that of the commercial fishery in order to describe patterns of genetic structure and genetic variation within and among the harvested component. We also included Arctic Char from more geographically distant sampling locations to provide a spatial context for genetic stock structuring in the region. Overall, we found moderate but significant structure across the entire study area. In contrast, commercially harvested stocks were weakly differentiated, especially among the stocks that are considered part of the Wellington Bay complex. We propose several hypotheses for this weak differentiation, including (1) our sampling design that mirrored the commercial harvest, (2) high rates of potential gene flow, and (3) large effective population sizes. Our results may have important implications for commercial and subsistence fisheries management, including the notion that there are several potential units of conservation below the species level.

Received September 29, 2015; accepted August 17, 2016 Published online November 28, 2016
Adolescent Depression
Authors: Corcoran Jacqueline
Published: November 2016

Rates of depression increase during adolescence, putting youth at possible risk for suicide, future episodes, and impaired functioning in multiple life domains. Diagnosis and Assessment, Epidemiology and Prevalence, Risk Factors, Treatment, and Prevention are addressed in this entry. Although depression in children is relatively rare, in adolescence the incidence of depression increases considerably, with a rate of about 5.7 percent, although studies vary. The Diagnostic and Statistical Manual of Mental Disorders, or DSM (American Psychiatric Association 2013, cited under Diagnosis and Assessment), describes and categorizes mental disorders and is widely used by mental health professionals in the United States. The depressive disorders that pertain to adolescents include major depressive disorder, persistent depressive disorder, and disruptive mood dysregulation. Major depressive disorder describes at least a two-week period during which a person experiences a depressed mood or loss of interest in nearly all life activities, with five or more symptom categories being represented. Persistent depressive disorder represents a general personality style featuring ongoing symptoms that are similar to, but less intense than, those of major depression. A new diagnosis created in the fifth edition of the DSM, (the DSM-5) is disruptive mood dysregulation disorder, which is a twelve-month pattern of behavior that is experienced daily, consisting of temper outbursts and irritable and angry mood starting before the age of ten. The system used outside of the United States and worldwide for classifying both mental health and medical conditions is the International Statistical Classification of Diseases and Related Health Problems (ICD-10), published by the World Health Organization (see World Health Organization 1992, cited under Diagnosis and Assessment). The depressive disorders and their criteria are similar between the, with some minor differences.
Key Figures: North American Environmental Scientist Activists
Authors: Wohl Ellen
Published: November 2016

Environmental scientist activist is not an established phrase. Here it designates individuals who begin their careers as professional scientists and become concerned about the loss of natural ecosystems or species, or environmental degradation and associated health effects. This concern gives rise to activism on behalf of environmental protection and enhancing public awareness of environmental issues. For some, activism takes the form of writing for a popular audience. Others become widely recognized figures who appear in documentary films or television shows. Some of the scientist activists are associated with a particular environment, such as Eugenie Clark and Sylvia Earle as advocates for protection of marine ecosystems. Others are noted for their expertise and activism in relation to a specific issue, such as Theo Colborn, Sandra Steingraber, and Devra Davis for environmental contamination or Hansen for climate change. Dian Fossey and Birutė Galdikas are associated with particular groups of animals—gorillas and chimpanzees, respectively. Others, such as Aldo Leopold and E. O. Wilson, are associated with a broader spectrum of environmental issues. Some of the individuals in this article speak out primarily based on their own research, whereas others have only a brief research career and draw from a wider base of published studies. Scientist activists are largely a 20th- and 21st-century phenomenon. Although scientifically trained individuals such as George Perkins Marsh argued for environmental preservation during the 19th century, environmental advocacy by professional scientists became more widespread during the 20th century. This likely reflects the rapid increase in the number of professional scientists since World War II, as well as widespread environmental degradation. As more scientists trained in chemistry, biology, and other environmental disciplines become aware of the threats facing ecosystems, wild organisms, and human health, the urge to communicate this awareness drives environmental activism. Two themes emerge: the fundamental reliance of humans on natural ecosystems and ecosystem services, and the shared traits of humans and other organisms. From Leopold’s articulation of the land ethic, to Wilson’s arguments for protecting biodiversity, the scientists who have become activists argue for the critical importance of protecting functional ecosystems in order to insure human survival. In addition, humans have traditionally distinguished themselves from other species based on traits such as communication, construction and use of tools, learned behavior, and distinctive personalities. As biologists including Fossey, Galdikas, and Schaller have documented the same traits in other species and raised public awareness of these traits, many people have begun to rethink the intrinsic right of other species to exist.
Social Network Analysis
Authors: Everett Martin , Crossley Nick , Bellotti Elisa
Published: November 2016

Social network analysis (SNA) is a methodology for capturing, storing, visualizing and analyzing relational data; that is, data concerning relations between specified entities (e.g., individuals, organizations, nations) and patterns of connection within populations of such entities. As such it stands in contrast to most standard social scientific approaches, which typically focus upon the attributes of such entities (although attributes can be included in SNA). Interest in social relations, their properties and effects, stretches back to the origins of social science and indeed even further back to the earliest social philosophies, and the origins of SNA itself can be traced back at least as far as the 1930s. The perspective has enjoyed a huge boost in recent years, however, not least as advances in technology have increased the computing power routinely available to social scientists. There are a number of good software packages today which offer users a comprehensive range of powerful analytic routines. This review covers: (1) data collection, (2) network measures, (3) roles and positions, (4) ego networks, (5) statistical methods, (6) mixed methods, (7) social capital, (8) small worlds, (9) large, complex and multimode data, (10) visualization, and (11) cohesive subgroups/community detection.
Thomas Wentworth Higginson
Authors: Petrulionis Sandra
Published: November 2016

Thomas Wentworth Higginson (b. 1823–d. 1911) was a native of Cambridge, Massachusetts, and a graduate of Harvard College (1841) and Harvard Divinity School (1847). A prolific author and popular lecturer, Higginson was also a Unitarian minister, an abolitionist activist, a soldier, an editor, a women’s rights leader, and a literary critic. His reputation has largely been based on his relationship with and co-editing (with Mabel Loomis Todd) of the poet Emily Dickinson as well as on his antislavery activism and command of the First South Carolina Volunteers (later the 33rd US Colored Infantry Regiment), the first military unit composed of freed slaves during the Civil War. More recently, critical attention has focused on specific writings in Higginson’s extensive literary canon. In his wide-ranging articles, Higginson addressed topics of interest in 19th-century America—from transcendentalism, physical health, abolitionism, and women’s rights to US and transatlantic literary culture, Civil War experiences, biography, and history, in addition to, albeit fewer in number, works of fiction and poetry. His articles appeared regularly in the Atlantic Monthly, Scribner’s, Putnam’s Monthly, Independent, Century, Harper’s Monthly, and other periodicals. He also contributed hundreds of columns addressing women’s rights and other political subjects to the Nation, the Radical, and the Boston Woman’s Journal. Higginson’s best-selling work was a classroom text, Young Folks’ History of the United States (1875), while his Civil War volume, Army Life in a Black Regiment (1870), has become a staple of today’s college syllabi. His only novel, Malbone (1869), is a fairly formulaic romance, set in New England, that received little critical attention. During the antebellum era, his liberal Unitarian ministry reflected his radical abolitionism as well as the transcendentalism of Ralph Waldo Emerson and Theodore Parker. After the Civil War, Higginson settled in Newport, Rhode Island, with his first wife, Mary Channing Higginson, where he cultivated a staid postbellum literary identity frequently characterized as “genteel.” He was closely involved with the women’s rights activists who organized the American Woman Suffrage Association in 1868, and for many years he penned a column on women’s issues for this organization’s Woman’s Journal. Higginson is known for encouraging young literary aspirants, particularly women, who in addition to Dickinson, include Harriet Prescott Spofford, Helen Hunt Jackson, and Emma Lazarus. His Life of Margaret Fuller Ossoli (1884) offers a sympathetic treatment of Fuller’s genius and importance. In 1879, following the death of his first wife two years prior, Higginson married Mary Thacher Higginson; their daughter, Margaret, was born in 1881. Toward the end of his life, Higginson joined the likes of Upton Sinclair, Charlotte Perkins Gilman, Jack London, and others in his support for the newly organized Intercollegiate Socialist Society.
Atmospheric Teleconnections
Authors: Goodrich Gregory
Published: November 2016

Climate teleconnections are commonly defined as low-frequency variability in the atmosphere and oceans, while weather is defined as random high-frequency variability in the atmosphere. A secondary definition of teleconnections is that of significant correlations of climatological variables at widely separated points on the earth, showing evidence of preferred trough/ridge positions. These preferred modes of variability can be measured through the use of indices to quantify flow patterns associated with the teleconnection. The indices can then be correlated with climate variables across the globe that display significant relationships. Teleconnections can have periods ranging from several weeks to several decades and can affect temperature, precipitation, storm tracks, severe weather, and drought. The strength and coherence of a teleconnection’s signal often changes over time, and evidence suggests that the phase of the multidecadal ocean oscillations in the Atlantic and Pacific are often the cause. Extreme weather is often influenced by teleconnection patterns that cause persistent weather in various locations. Teleconnections are often a useful tool for seasonal forecasters and are commonly used in predicting commodity and energy trading markets. While many teleconnections were originally empirically derived, there has been progress in understanding the physical mechanisms behind many of them, which has helped to improve their predictability. There is much uncertainty regarding how climate change will affect many teleconnections, and this is an area of active research. The objective of this article is to introduce atmospheric and oceanic teleconnections that commonly affect weather patterns in the United States and around the globe. The article will introduce the history of how teleconnections were discovered and the statistics of how the index that determines the phase of the teleconnection was calculated. Several oceanic and atmospheric teleconnections will be discussed along with their known impacts on weather and climate.
Guomindang (1912–1949)
Authors: Samarani Guido , De Giorgi Laura
Published: November 2016

Studies on the Chinese Nationalist Party, the Zhongguo Guomindang (GMD), have focused on some fundamental questions. The first has concerned its political and ideological roots. The GMD was built in 1912 when Sun Yat-sen directed the transformation of the Tongmenghui into a centralized, democratic political party. In 1913, however, the ex-Qing minister and general, Yuan Shikai, became the president of the Republic of China and ordered the dissolution of the GMD. In 1919 the GMD was revived by Sun, but only in 1923 did the party reaffirm its role. In the early Republic, the GMD developed in a political culture in which factions and personal connections were fundamental, causing large disagreement about its policy and ideology. In the early 1920s, Comintern representatives helped to reorganize the GMD in a Leninist-style party, setting basic approaches for bilateral cooperation, to include the recently established Chinese Communist Party (CCP). The GMD was restructured and a modern military force was created. The party’s ideology was, on the contrary, rather homegrown: the Three People’s Principles were elaborated into a political platform that targeted warlordism and imperialism. From 1926 on, the Guomindang, with the support of the Soviet advisers and the CCP, brought the warlord era to an end and, to a great extent, unified China; after Sun’s death in 1925, Chiang Kai-shek (Jiang Jieshi) rose to national power. The second area of investigation has concerned GMD’s performance in state building and governance. In 1928, after the end the Northern Expedition and the GMD-CCP split, Chiang and the GMD established a national government in Nanjing, which lasted about ten years (1928–1937, the so-called Nanjing decade), before the start of China’s war of resistance against Japan. The war years (1937–1945) saw the GMD-CCP United Front, which was largely ineffective; the relocation of the capital to Chongqing; and the birth of a collaborationist government headed by Wang Jingwei. In the late 1940s, a final battle between the GMD and the CCP resulted in the founding of the People’s Republic of China in 1949 and in the retreat of the Guomindang to Taiwan. Scholars have debated on the GMD’s capacity, arguing either that the modest but definite successes in unification and a variety of modernization projects would in the long run have produced a stable and prosperous country, had not the Japanese invaded China, or, on the contrary, emphasizing how GMD regime’s authoritarianism, corruption, and incompetence as well as Chiang’s policy produced a demoralizing effect on the party and a growing dissatisfaction within society. For many decades, studies on the GMD have been informed by the Cold War–era divisions and the basic orientations of Chinese historiography during the Maoist period. Recently new trends have emerged offering deeper insights into several questions, which include a more reliable evaluation of Chiang Kai-shek’s role.
Whole genome sequencing to investigate a putative outbreak of the virulent community-associated methicillin-resistant Staphylococcus aureus ST93 clone in a remote Indigenous community
Authors: Meumann Ella M. , Andersson Patiyan , Yeaman Fiona , Oldfield Sarah , Lilliebridge Rachael , Bentley Stephen D. , Krause Vicki , Beaman Miles , Currie Bart J. , Holt Deborah C. , Giffard Philip M. , Tong Steven Y. C.
Published: November 2016

We report two cases of severe pneumonia due to clone ST93 methicillin-resistant Staphylococcus aureus (MRSA) presenting from a remote Australian Indigenous community within a 2-week period, and the utilization of whole genome sequences to determine whether these were part of an outbreak. S. aureus was isolated from 12 of 92 nasal swabs collected from 25 community households (including the two index households); one isolate was ST93. Three of five skin lesion S. aureus isolates obtained at the community were ST93. Whole genome sequencing of the ST93 isolates from this study and a further 20 ST93 isolates from the same region suggested that recent transmission and progression to disease had not taken place. The proximity in time and space of the two severe pneumonia cases is probably a reflection of the high burden of disease due to ST93 MRSA in this population where skin infections and household crowding are common.
Genome-Wide Association Study Reveals First Locus for Anorexia Nervosa and Metabolic Correlations
Authors: Duncan E. L. , Thornton L. M. , Hinney A. , Daly M. J. , Sullivan P. F. , Zeggini E. , Breen G. , Bulik C. M.
Published: November 2016

Anorexia nervosa (AN) is a serious eating disorder characterized by restriction of energy intake relative to requirements, resulting in abnormally low body weight. It has a lifetime prevalence of approximately 1%, disproportionately affects females1,2, and has no well replicated evidence of effective pharmacological or psychological treatments despite high morbidity and mortality2. Twin studies support a genetic basis for the observed aggregation of AN in families3, with heritability estimates of 48%-74%4. Although initial genome-wide association studies (GWASs) were underpowered5,6, evidence suggested that signals for AN would be detected with increased power5. We present a GWAS of 3,495 AN cases and 10,982 controls with one genome-wide significant locus (index variant rs4622308, p=4.3x10−9) in a region (chr12:56,372,585-56,482,185) which includes six genes. The SNP-chip heritabilityof AN from these data is 0.20 (SE=0.02), suggesting that a substantial fraction of the twin-based heritability stems from common genetic variation. Using these GWAS results, we also find significant positive genetic correlations with schizophrenia, neuroticism, educational attainment, and HDL cholesterol, and significant negative genetic correlations with body mass, insulin, glucose, and lipid phenotypes. Our results support the reconceptualization of AN as a disorder with both psychiatric and metabolic components.
Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
Authors: Sundaramoorthy Ramasubramanian , Hughes Amanda L. , Singh Vijender , Wiechens Nicola , Ryan Daniel P. , El-Mkami Hassane , Petoukhov Maxim , Svergun Dmitri I. , Treutlein Barbara , Fischer Monika , Michaelis Jens , Böttcher Bettina , Norman David G. , Owen-Hughes Tom
Published: November 2016

The yeast Chd1 protein acts to position nucleosomes across genomes. Here we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state the DNA binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavourable alignment of C-terminal DNA binding region in solution contributes to an auto-inhibited state.
Kinetics of multi-substrate inBeauveriabassiana JUCHE22
Authors: Mondal Subhoshmita , Majumdar Sarangam
Published: November 2016

The pattern of the biomass specific growth rate is an important focus for many biotechnological applications. Several control strategies have been employed to describe version of the exponential phase of growth of microorganisms. Moreover, in some bioprocesses there is more than one feeding substrates required for the specific growth. Hence, the problem of estimating multiple substrate consumption rates together with the specific growth rate of the microorganism becomes applicable. In this context, the dynamics behaviour of fed-batch process with multiple substrates (dextrose and peptone) and kinetics is further investigated inBeauveria bassiana. Different features of the proposed model are assessed by numerical simulation in different scenarios.
Ecological Interactions and the Netflix Problem
Authors: Desjardins-Proulx Philippe , Laigle Idaline , Poisot Timothée , Gravel Dominique
Published: November 2016

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Species interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore theKnearest neighbour approach, with a special emphasis on recommendation, along with other machine learning techniques. Recommenders are algorithms developed for companies like Netflix to predict if a customer would like a product given the preferences of similar customers. These machine learning techniques are well-suited to study binary ecological interactions since they focus on positive-only data. We also explore how theKnearest neighbour approach can be used with both positive and negative information, in which case the goal of the algorithm is to fill missing entries from a matrix (imputation). By removing a prey from a predator, we find that recommenders can guess the missing prey around 50% of the times on the first try, with up to 881 possibilities. Traits do not improve significantly the results for theKnearest neighbour, although a simple test with a supervised learning approach (random forests) show we can predict interactions with high accuracy using only three traits per species. This result shows that binary interactions can be predicted without regard to the ecological community given only three variables: body mass and two variables for the species’ phylogeny. These techniques are complementary, as recommenders can predict interactions in the absence of traits, using only information about other species’ interactions, while supervised learning algorithms such as random forests base their predictions on traits only but do not exploit other species’ interactions. Further work should focus on developing custom similarity measures specialized to ecology to improve theKNN algorithms and using richer data to capture indirect relationships between species.
Genome sequencing and analysis of the first spontaneous Nanosilver resistant bacteriumProteus mirabilisstrain SCDR1
Authors: Saeb Amr T. M. , Al-Rubeaan Khalid A. , Abouelhoda Mohamed , Selvaraju Manojkumar , Tayeb Hamsa T.
Published: November 2016

Background

P. mirabilisis a common uropathogenic bacterium that can cause major complications in patients with long-standing indwelling catheters or patients with urinary tract anomalies. In addition,P. mirabilisis a common cause of chronic osteomyelitis in Diabetic foot ulcer (DFU) patients. We isolatedP. mirabilis SCDR1from a Diabetic ulcer patient. We examinedP. mirabilisSCDR1 levels of resistance against Nano-silver colloids, the commercial Nano-silver and silver containing bandages and commonly used antibiotics. We utilized next generation sequencing techniques (NGS), bioinformatics, phylogenetic analysis and pathogenomics in the characterization of the infectious pathogen.

Results

P. mirabilis SCDR1is a multi-drug resistant isolate that also showed high levels of resistance against Nano-silver colloids, Nano-silver chitosan composite and the commercially available Nano-silver and silver bandages. TheP. mirabilis-SCDR1 genome size is 3,815,621 bp. with G+C content of 38.44%.P. mirabilis-SCDR1 genome contains a total of 3,533 genes, 3,414 coding DNA sequence genes, 11, 10, 18 rRNAs (5S, 16S, and 23S), and 76 tRNAs. Our isolate contains all the required pathogenicity and virulence factors to establish a successful infection.P. mirabilisSCDR1 isolate is a potential virulent pathogen that despite its original isolation site, wound, it can establish kidney infection and its associated complications.P. mirabilis SCDR1contains several mechanisms for antibiotics and metals resistance including, biofilm formation, swarming mobility, efflux systems, and enzymatic detoxification.

Conclusion

P. mirabilis SCDR1is the first reported spontaneous Nanosilver resistant bacterial strain.P. mirabilisSCDR1 possesses several mechanisms that may lead to the observed Nanosilver resistance.
Testing the neutral hypothesis of phenotypic evolution
Authors: Ho Wei-Chin , Ohya Yoshikazu , Zhang Jianzhi
Published: November 2016

It is generally accepted that a large fraction of genomic sequence variations within and between species are neutral or nearly so1. Whether the same is true for phenotypic variations is a central question in biology2-7. On the one hand, numerous phenotypic adaptations have been documented2,8,9and even Kimura, the champion of the neutral theory of molecular evolution, believed in widespread adaptive phenotypic evolution1. On the other hand, phenotypic studies are strongly biased toward traits that are likely to be adaptive9, contrasting genomic studies that are typically unbiased. It is thus desirable to test the neutral hypothesis of phenotypic evolution using traits irrespective of their potential involvement in adaptation. Here we present such a test for 210 morphological traits measured in multiple strains of the yeastSaccharomyces cerevisiaeand two related species. Our test is based on the premise that, under neutrality, the rate of phenotypic evolution declines as the trait becomes more important to fitness, analogous to the neutral paradigm that functional genes evolve more slowly than functionless pseudogenes10. Neutrality is rejected in favor of adaptation if important traits evolve faster than less important ones, parallel to the demonstration of molecular adaptation when a functional gene evolves faster than pseudogenes. After controlling for the mutational size, we find faster evolution of more important morphological traits within and between species. By contrast, an analysis of 3466 yeast gene expression traits fails to reject neutrality. Thus, yeast morphological evolution is largely adaptive, but the same may not apply to other classes of phenotypes.
Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation
Authors: Belaghzal Houda , Dekker Job , Gibcus Johan H.
Published: November 2016

Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (Kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and TADs, as well as high-resolution conformational features such as DNA loops.
Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance
Authors: Emad Amin , Woese Carl R. , Cairns Junmei , Kalari Krishna R. , Wang, M.D. Liewei , Sinha Saurabh
Published: November 2016

Background

Identification of genes whose basal mRNA expression predicts the sensitivity of tumor cells to cytotoxic treatments can play an important role in individualized cancer medicine. It enables detailed characterization of the mechanism of action of drugs. Furthermore, screening the expression of these genes in the tumor tissue may suggest the best course of chemotherapy or a combination of drugs to overcome drug resistance.

Results

We developed a computational method called ProGENI to identify genes most associated with the variation of drug response across different individuals, based on gene expression data. In contrast to existing methods, ProGENI also utilizes prior knowledge of protein-protein and genetic interactions, using random walk techniques. Analysis of two relatively new and large datasets including gene expression data on hundreds of cell lines and their cytotoxic responses to a large compendium of drugs reveals a significant improvement in prediction of drug sensitivity using genes identified by ProGENI compared to other methods. Our siRNA knockdown experiments on ProGENI-identified genes confirmed the role of many new genes in sensitivity to three chemotherapy drugs: cisplatin, docetaxel and doxorubicin. Based on such experiments and extensive literature survey, we demonstrate that about 73% our top predicted genes modulate drug response in selected cancer cell lines. In addition, global analysis of genes associated with groups of drugs uncovered pathways of cytotoxic response shared by each group.

Conclusions

Our results suggest that knowledge-guided prioritization of genes using ProGENI gives new insight into mechanisms of drug resistance and identifies genes that may be targeted to overcome this phenomenon.
Determination of copper nanoparticle size distributions with total reflection X-ray fluorescence spectroscopy
Authors: Singh Andy , Luening Katharina , Brennan Sean , Homma Takayuki , Kubo Nobuhiro , Nowak Stanisław H. , Pianetta Piero
Published: November 2016

Total reflection X-ray fluorescence (TXRF) analysis is extensively used by the semiconductor industry for measuring trace metal contamination on silicon surfaces. In addition to determining the quantity of impurities on a surface, TXRF can reveal information about the vertical distribution of contaminants by measuring the fluorescence signal as a function of the angle of incidence. In this study, two samples were intentionally contaminated with copper in non-deoxygenated and deoxygenated ultrapure water (UPW) resulting in impurity profiles that were either atomically dispersed in a thin film or particle-like, respectively. The concentration profile of the samples immersed into deoxygenated UPW was calculated using a theoretical concentration profile representative of particles, yielding a mean particle height of 16.1 nm. However, the resulting theoretical profile suggested that a distribution of particle heights exists on the surface. The fit of the angular distribution data was further refined by minimizing the residual error of a least-squares fit employing a model with a Gaussian distribution of particle heights about the mean height. The presence of a height distribution was also confirmed with atomic force microscopy measurements.
Synchrotron-based phase-sensitive imaging of leaves grown from magneto-primed seeds of soybean
Authors: Fatima A. , Kataria S. , Baghel L. , Guruprasad K. N. , Agrawal A. K. , Singh B. , Sarkar P. S. , Shripathi T. , Kashyap Y.
Published: November 2016

Experiments were conducted to study the effects of static magnetic fields (SMFs) on the venation network of soybean leaves using the synchrotron-based X-ray micro-imaging technique. The seeds of soybean (Glycine max, variety JS-335) were pretreated with different SMFs from 50 to 300 mT in steps of 50 mT for 1 h. The phase-contrast images obtained showed that, as the strength of the SMF increased, the area, width of the midrib, area of the midrib and minor vein of the middle leaflets of third trifoliate leaves also increased up to the SMF strength of 200 mT (1 h) and decreased thereafter. Quantification of the major conducting vein also showed the differences in the major and minor vein structures of the soybean leaves as compared with control leaves. Further, the phase-retrieval technique has been applied to make the segmentation process easy and to quantify the major and minor veins in the venation network. The width and area of midrib enhancement by pre-treatment with SMF implies an enhancement in the uptake of water, which in turn causes an increased rate of photosynthesis and stomatal conductance.