bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Proper is whatever people make it”
Authors: Valentinsson Mary-Caitlyn 
Published: July 2018

Abstract
This study analyzes a family dinnertime conversation in order to understand how language ideologies are created through everyday talk. Drawing on Conversation/Discourse Analysis and linguistic anthropology, this study address three questions central to this volume: (1) What and how do linguistic forms convey a speaker’s subjectivity and identity in the local context of interaction and to what level of language do they belong? (2) Which forms position individual speakers or groups of speakers socially and culturally (because of their association with particular situations or situational dimensions)? And (3), what are the socio-cultural norms for language usage, which enable speakers to represent their identities? I argue that a range of linguistic stance-taking strategies, and the way these strategies create positionalities for interlocutors, illustrate the relationship between ideology and everyday interaction. This paper also argues for the importance of understanding the sociocultural context of talk in order to interpret interactional data.
(And yet) another proposal for ser/estar
Authors: Mangialavori Rasia M. Eugenia 
Published: July 2018

This paper puts forward an l-syntactic account of non-trivially alternating copulas ser/estar building on incorporation of a prepositional head (p*). I propose that p* is to be seen as a locus of encoding and variation of the relevant properties whereby ser/estar diverge, but also as the element constraining selection and interpretation of the predicate.
First, I use the distinction between telicity and boundedness as a starting point for developing a reformulation of the Hale-and-Keyserian analysis of ser/estar that supports a new typology of p heads within the Central Coincidence domain. This is important to capture wider sets of corpus and analytic data, but also in order to reflect an adequate division of work between verbal (Aktionsart) and constructional aspect. Then, I propose a novel implementation based on p-conflation and Hyponym Argument Relations. If correct, the analysis handles different facts and at the same time positions ser/estar into a much ampler frame.
Two types of trouble with questions
Authors: Kim Stephanie Hyeri 
Published: July 2018

Abstract
Most previous studies of Korean conversation have focused on clause-
or sentence-final elements to describe various interactional
strategies of conversationalists. This chapter demonstrates that the
beginnings of a turn in Korean are also an interactionally important
place, and provides a comparative analysis of two turn-initial
particles used in responses to questions: kulssey
and kulenikka. Both particles can be translated as
well in the target sequential position and
index that there is some trouble with the question. However, each
particle is used for addressing a particular type of trouble with
the preceding question and for indexing a specific upcoming action.
This chapter includes an account for how the particles may have
acquired these functions, and a brief comparison of the particles to
the comparable English particle well.
A-prefaced responses to inquiry in Japanese
Authors: Hayashi Makoto , Hayano Kaoru 
Published: July 2018

Abstract
This study explores the stances communicated by two turn-initial
particles in Japanese, a and eh,
when they are used to preface responses to inquiry. The particle
a comes close in its usage to
oh in English and is often used to acknowledge
the receipt of new and/or unexpected information.
Eh is similar to a in that it
indicates that the information being received is unexpected;
however, it is often employed in contexts where its producer
problematizes or resists what the prior speaker has just said, such
as in other-initiated repair and disagreements. We compare the
workings of these two particles in the context of prefacing
responses to inquiry and show that, while
a-prefaced responses generally embody moves that
are affiliative with the prior speaker, eh-prefaced
responses convey more disaffiliative stances. Based on our findings,
we suggest that there is a division of labor between
a-prefacing and eh-prefacing
of question responses in Japanese and that what is performed by one
particle in one language (oh in English) may be
carried out by two particles in another (a and
eh in Japanese).
Treating something as self-evident
Authors: Weidner Matylda 
Published: July 2018

Abstract
This chapter offers a detailed sequential examination of the usage of
the turn-initial Polish particle no in responsive
actions. It demonstrates that no represents a
particular kind of epistemic stance, where it contributes a “my
side” positioning of the no speaker, and in this
way participates in the local management of epistemic relations
between speakers of Polish. Drawing on the analysis of data from
both institutional and ordinary interactions, I demonstrate that
stand-alone no and no-prefaces
index the stance of the current speaker towards the prior speaker’s
turn or action. No operates on three layers, which
are invoked by the particular sequential and activity contexts in
which the particle occurs. The primary function of
no is to treat the content of the prior
speaker’s turn as already known or self-evident. Second, associated
with that treatment, no invokes its speaker’s
“my-side” perspective and alerts the recipient to a possible
incongruity between the no speaker’s epistemic
status vis-à-vis the recipient’s perspective. The third layer is
sequential in character and drawing on the affordances created by
the two other epistemic and stance-related layers, exploits these
basic interactional capacities of no in a further
direction. When this happens, a no-prefaced action
can set a given piece of knowledge aside and hence contribute to
sequence closure and coincide with a topic and/or an activity shift.
Based on the analysis of both the preceding and subsequent talk
surrounding no, this chapter illustrates some
systematic regularities related to the usage of no,
which offer empirical evidence that no is
implicated in foreshadowing epistemic stance in contexts of
epistemic incongruence.
Calibrating an agnostic epistemic stance in Swedish
conversation
Authors: Lindström Anna 
Published: July 2018

Abstract
Conversation analytic research on turn-initial particles has by and
large examined turn-initial items that are language (or language
family) specific such as the English well, the
Finnish niin, the French voilà,
and the German naja. This chapter by contrast,
explores the turn-initial use of a word that was imported as a loan
from English to Swedish, namely okay, in Swedish
okej. The data is drawn from interactions
between clients and administrators at the Swedish Board for Study
Support. I have analyzed telephone calls where clients are inquiring
about how to apply for a new loan or negotiating the payback of an
existing loan. The discourse marker okej ‘okay’ is
recurrent in these materials. Okej can be used by
itself as a first pair part, a second pair part, or a sequence
closing third. It can also be embedded within larger turns. This
chapter is based on a collection where okej is used
as a turn preface. By analysing the sequential context, action
implementation, and sequential trajectory of
okej-prefaced turns, I show that
okej-prefacing is used by call takers as an
agnostic marker by registering the information provided by the
caller without either endorsing it as true or dismissing it as
false.
BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains
Authors: Jiao Chuan , Yan Pengpeng , Xia Cuihua , Shen Zhaoming , Tan Zexi , Tan Yanyan , Wang Kangli , Jiang Yi , Huang Lingling , Dai Rujia , Wei Yu , Xia Yan , Meng Qingtuan , Ouyang Yanmei , Yi Liu , Duan Fangyuan , Dai Jiacheng , Zhao Shunan , Liu Chunyu , Chen Chao 
Published: July 2018

Abstract

Summary
Gene expression changes over the lifespan and varies among different tissues or cell types. Gene co-expression also changes by sex, age, different tissues or cell types. However, gene expression under the normal state and gene co-expression in the human brain has not been fully defined and quantified. Here we present a database named Brain EXPression Database (BrainEXP) which provides spatiotemporal expression of individual genes and co-expression in normal human brains. BrainEXP consists of 4567 samples from 2863 healthy individuals gathered from existing public databases and our own data, in either microarray or RNA-Seq library types. We mainly provide two analysis results based on the large dataset: (i) basic gene expression across specific brain regions, age ranges and sexes; (ii) co-expression analysis from different platforms.

Availability and implementation
http://www.brainexp.org/

Supplementary information
Supplementary data are available at Bioinformatics online.
S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks
Authors: Yan Hongwei , Gunawan Andreas D M , Zhang Louxin 
Published: July 2018

Abstract

Motivation
Comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations (vertical evolution) and genomic material transfers between individuals of different lineages (reticulate transfer). This has motivated biologists to use phylogenetic networks and other general models to study genome evolution. Two fundamental algorithmic problems arising from verification of phylogenetic networks and from computing Robinson-Foulds distance in the space of phylogenetic networks are the tree and cluster containment problems. The former asks how to decide whether or not a phylogenetic tree is displayed in a phylogenetic network. The latter is to decide whether a subset of taxa appears as a cluster in some tree displayed in a phylogenetic network. The cluster containment problem (CCP) is also closely related to testing the infinite site model on a recombination network. Both the tree containment and CCP are NP-complete. Although the CCP was introduced a decade ago, there has been little progress in developing fast algorithms for it on arbitrary phylogenetic networks.

Results
In this work, we present a fast computer program for the CCP. This program is developed on the basis of a linear-time transformation from the small version of the CCP to the SAT problem.

Availability and implementation
The program package is available for download on http://www.math.nus.edu.sg/∼matzlx/ccp.
microRNA-184 and Its lncRNA Sponge UCA1 are Induced in Wounded Keratinocytes in a Store-Operated Calcium Entry-Dependent Manner
Authors: Richardson Adam , Owens Daniel , Ross Kehinde 
Published: July 2018

ABSTRACTEmerging evidence implicates microRNAs (miRNA) in the regulation of keratinocyte migration. However, the putative roles of microRNA-184 (miR-184) in keratinocyte migration have not been examined. Here, we show that miR-184 expression was elevated following wounding of human keratinocyte monolayers. The induction of miR-184 was dependent on store-operated calcium entry (SOCE) as it was abolished by pharmacologic SOCE blockers. The long non-coding RNA urothelial cancer associated 1 (UCA1), which is thought to acts as a sponge or competing endogenous RNA (ceRNA) against miR-184 was also induced in scratched monolayers. Induction of UCA1 was impaired, but not abolished, by SOCE inhibition. Transfection of keratinocytes with a miR-184 mimic stimulated migration in scratch assays, whereas inhibition of miR-184 dampened the ability of keratinocytes to migrate. Together, our data suggest, for the first time, that SOCE promotes miR-184 induction in wounded monolayers to support keratinocyte migration while also increasing lncRNA UCA1 expression, which may in turn regulate miR-184 activity in keratinocytes.
Prospective Study of Polygenic Risk, Protective Factors, and Incident Depression Following Combat Deployment in US Army Soldiers
Authors: Choi Karmel W. , Chen Chia-Yen , Ursano Robert J. , Sun Xiaoying , Jain Sonia , Kessler Ronald C. , Koenen Karestan C. , Wang Min-Jung , Wynn Gary H. ,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Laura Campbell-Sills, Stein Murray B. , Smoller Jordan W. 
Published: July 2018

AbstractBackgroundWhereas genetic susceptibility increases risk for major depressive disorder (MDD), non-genetic protective factors may mitigate this risk. In a large-scale prospective study of US Army soldiers, we examined whether trait resilience and/or unit cohesion could buffer against the onset of MDD following combat deployment, even in soldiers at high polygenic risk.MethodsData were analyzed from 4,182 soldiers of European ancestry assessed before and after their deployment to Afghanistan. Incident MDD was defined as no MDD episode at predeployment, followed by a MDD episode following deployment. Polygenic risk scores were constructed from the largest available MDD genome-wide association study. We first examined main effects of the MDD PRS and each protective factor on incident MDD. We then tested effects of each protective factor on incident MDD across strata of polygenic risk.ResultsPolygenic risk showed a dose-response relationship to depression, such that soldiers at high polygenic risk had greatest odds for incident MDD. Both unit cohesion and trait resilience were prospectively associated with reduced risk for incident MDD. Notably, the protective effect of unit cohesion persisted even in soldiers at highest polygenic risk.ConclusionsPolygenic risk was associated with new-onset MDD in deployed soldiers. However, unit cohesion—an index of perceived support and morale—was protective against incident MDD even among those at highest genetic risk, and may represent a potent target for promoting resilience in vulnerable soldiers. Findings illustrate the value of combining genomic and environmental data in a prospective design to identify robust protective factors for mental health.
CRISPR-Cas12b-assisted nucleic acid detection platform
Authors: Li Linxian , Li Shiyuan , Wang Jin 
Published: July 2018

AbstractRapid molecular diagnostic technology is very useful in many areas, including public health, environmental testing and criminal investigation. We recently showed that Cas12a had trans-cleavage activity upon collateral single-stranded DNA (ssDNA), with which the HOLMES platform (one-HOur Low-cost Multipurpose highly Efficient System) was developed. Here, we combine the thermophilic Cas12b, which also has the ssDNA trans-cleavage activity, with Loop-Mediated Isothermal Amplification (LAMP), and create HOLMESv2. In HOLMESv2, LAMP amplification and Cas12b trans-cleavage can be integrated into a one-step system with a constant temperature, which therefore brings much convenience in nucleic acid detection. Moreover, we also simplify the RNA detection procedures in HOLMESv2, using an RNA-dependent DNA polymerase for amplification and therefore omitting an extra reverse transcription step.One Sentence SummaryWe combine LAMP and Cas12b to develop HOLMESv2 for conveniently detecting target nucleic acid in a one-step approach.
Systems Biology Understanding of the Effects of Lithium on Cancer
Authors: Ge Weihao , Jakobsson Eric 
Published: July 2018

AbstractLithium has many widely varying biochemical and phenomenological effects, suggesting that a systems biology approach is required to understand its action. Multiple lines of evidence point to lithium as a significant factor in development of cancer, showing that understanding lithium action is of high importance. In this paper we undertake first steps towards a systems approach by analyzing mutual enrichment between the interactomes of lithium-sensitive enzymes and the pathways associated with cancer. This work integrates information from two important databases, STRING and KEGG pathways. We find that for the majority of cancer pathways the mutual enrichment is many times greater than chance, reinforcing previous lines of evidence that lithium is an important influence on cancer.
Deriving general conditions and mechanisms for division of labor using the cell-based simulator gro
Authors: Gregorio-Godoy Paula , del Pulgar Guillermo Pérez , Rodríguez-Regueira Marcos , Rodríguez-Patón Alfonso 
Published: July 2018

ABSTRACTDivision of Labor can occur as a consequence of a major evolutionary transition such as multicellularity but is also found in societies of similar individuals like microbes. It has been defined as a process that occurs when cooperating individuals specialize to carry out specific tasks in a distributed manner. This paper analyzes the conditions for division of labor to emerge as a beneficial evolutionary solution and proposes two novel mechanisms for this process to emerge as a consequence of cell communication in an isogenic group of cells. The study is conducted by means of the cell-based model gro that simulates the growth and interaction of cells in a two-dimensional bacterial colony. When the labor is social, like the production of a molecule that is publicly shared, simulation results indicate that division of labor provides higher fitness than individual labor if the benefits of specialization are accelerating. Two genetic networks that generate consensual and reversible specialization are presented and characterized. In the proposed mechanisms, cells self-organize through the exchange of certain molecules and coordinate behaviors at the local level without the requirements of any fitness benefits. In addition, the proposed regulatory mechanisms are able to create de novo patterns unprecedented to this date that can scale with size.
Habitat fragmentation and species diversity in competitive species communities
Authors: Rybicki Joel , Abrego Nerea , Ovaskainen Otso 
Published: July 2018

Abstract.Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. On the other hand, different empirical studies report contrasting patterns: some find positive and others negative effects of fragmentationper seon species richness.To explain this apparent disparity, we devise a stochastic, spatially-explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have a non-monotone and non-linear effect on the species diversity in competitive communities. When the total amount of habitat is large, fragmentationper setends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentationper sedecreases species diversity.
Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin
Authors: Rougemont Quentin , Carrier Anne , Leluyer Jeremy , Ferchaud Anne-Laure , Farrell John M. , Hatin Daniel , Brodeur Philippe , Bernatchez Louis 
Published: July 2018

AbstractUnderstanding the genetic and evolutionary impacts of fish stocking on wild populations has long been of interest as negative consequences such as reduced fitness and loss of genetic resources are commonly reported. Nearly five decades of extensive stocking of over a million Muskellunge (Esox masquinongy) in the Lower St. Lawrence River (Québec, Canada) was implemented by managers in an attempt to sustain a fishery. We investigated the effect of stocking on this native species’ genetic structure and allelic diversity in the St. Lawrence river and its tributaries as well as several stocked inland lakes. Using Genotype-By-Sequencing (GBS), we genotyped 643 individuals representing 22 sampling sites and combined this information with forward simulations to investigate the genetic consequences of stocking. Individuals native to the St. Lawrence watershed were genetically divergent from the sources used for stocking and both the St. Lawrence tributaries and inland lakes were also naturally divergent from the main stem. Empirical data and simulations revealed weak effects of stocking on admixture patterns within the St. Lawrence despite intense stocking in the past, whereas footprints of admixture were higher in the smaller stocked populations from tributaries and lakes. Altogether, our data suggests that selection against introgression has been relatively efficient within the large St. Lawrence River. In contrast, the smaller populations from adjacent tributaries and lakes still displayed stocking related admixture which apparently resulted in higher genetic diversity, suggesting that, while stocking stopped at the same time, its impact remained higher in these populations. Finally, the origin of populations from inland lakes that were established by stocking confirmed their close affinity with these source populations. This study illustrates the benefit of combining extensive genomic data with forward simulations for improved inferences regarding outcomes of population enhancement by stocking, as well as its relevance for fishery management decision making.
Identification of meiotic recombination through gamete genome reconstruction using whole genome linked-reads
Authors: Xu Peng ,   Human Genome Structural Variation Consortium, Chong Zechen 
Published: July 2018

AbstractMeiotic recombination (MR), which transmits exchanged genetic materials between homologous chromosomes to offspring, plays a crucial role in shaping genomic diversity in eukaryotic organisms. In humans, thousands of meiotic recombination hotspots have been mapped by population genetics approaches. However, direct identification of MR events for individuals is still challenging due to the difficulty in resolving the haplotypes of homologous chromosomes and reconstructing the gamete genome. Whole genome linked-read sequencing (lrWGS) can generate haplotype sequences of mega-base pairs (N50 ~2.5Mb) after computational phasing. However, the haplotype information is still isolated in a large number of fragmented genomic regions and limited by switch errors, impeding its further application in the chromosome-scale analysis. In this study, we developed a tool MRLR (Meiotic Recombination identification by Linked-Read sequencing) for the analysis of individual MR events. By leveraging trio pedigree information with lrWGS haplotypes, our pipeline is sufficient to reconstruct the whole human gamete genome with 99.8% haplotyping accuracy. By analyzing the haplotype exchange between homologous chromosomes, MRLR identified 462 high-resolution MR events in 6 human trio samples from the Genome In A Bottle (GIAB) and the Human Genome Structural Variation Consortium (HGSVC). In three datasets of the HGSVC, our results recapitulated 149 (92%) previously identified high-confident MR events and discovered 85 novel events. About half (40) of the new events are supported by single-cell template strand sequencing (Strand-seq) results. We found that 332 (71.9%) MR events co-localize with recombination hotspots (>10 cM/Mb) in human populations, and MR breakpoint regions are enriched in PRDM9 and DMC1 binding sites. In addition, 48% (221) breakpoint regions were detected inside a gene, indicating these MRs can directly affect the haplotype diversity of genic regions. Taken together, our approach provides new opportunities in the haplotype-based genomic analysis of individual meiotic recombination. The MRLR software is implemented in Perl and is freely available at https://github.com/ChongLab/MRLR.