bluuebunny/crossref_metadata_2025 huggingface dataset:
(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.
The role of L2 exposure in L3A
Authors: Stadt Rosalinde , Hulk Aafke , Sleeman Petra
Published: July 2018

In this study, we test the L2 Status Factor hypothesis (Bardel & Falk, 2007, 2012), which claims that the L2 is the preferred background language over the L1 in L3 acquisition (henceforth L3A), and we investigate the effect of L2 English exposure on the role of the L1 and the L2 in L3A. We examine how increased developmental L2 exposure changes L1/L2 influence in L3A by comparing third- to fourth-year secondary school students in the Netherlands who are enrolled in either an immersion or a traditional ‘regular’ secondary school programme. We look at verb placement where French differs from English or from Dutch, reporting data from a grammaticality judgement task.
Two types of trouble with questions
Authors: Kim Stephanie Hyeri
Published: July 2018

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

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

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

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.
The influence of process parameters in linear friction welded 30CrNiMo8 small cross-section: a modelling approach
Authors: Effertz Pedro dos Santos , Fuchs Franz , Enzinger Norbert
Published: July 2018

The linear friction welding process is a solid-state welding technology enabling high-quality joints in chains, thus competing with the currently in use flash butt welding process. In the present study, the effects of welding parameters were investigated, using 30CrNiMo8 small cross-section with 10 mm in diameter. To that end, a 2 k full factorial design was used. The influence of the process inputs was assessed experimentally and numerically using the commercial software DEFORM. A fairly good agreement was obtained between experiments and modelling. Some differences in the statistical effect of the parameters were observed regarding burn-off rate. Confirmation experiments were carried out to evaluate the adequacy of the attained regression models and good predictive ability was achieved.
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

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

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

Emerging 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

Background

Whereas 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.

Methods

Data 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.

Results

Polygenic 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.

Conclusions

Polygenic 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

Rapid 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 Summary

We 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

Lithium 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

Division 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

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

Understanding 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

Meiotic 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.
GWAS of QRS Duration Identifies New Loci Specific to Hispanic/Latino Populations Swenson Hispanic/Latino QRS GWAS
Authors: Swenson Brenton R. , Louie Tin , Lin Henry J. , MéndezGiráldez Raú , Below Jennifer E , Laurie Cathy C. , Kerr Kathleen F. , Highland Heather , Thornton Timothy A. , Ryckman Kelli K. , Kooperberg Charles , Soliman Elsayed Z. , Seyerle Amanda A. , Guo Xiuqing , Taylor Kent D. , Yao Jie , Heckbert Susan R. , Darbar Dawood , Petty Lauren E. , McKnight Barbara , Cheng Susan , Bello Natalie A. , Whitsel Eric A. , Hanis Craig L. , Nalls Mike A. , Evans Daniel S. , Rotter Jerome I. , Sofer Tamar , Avery Christy , Sotoodehnia Nona
Published: July 2018

Background

The electrocardiographically quantified QRS duration measures ventricular depolarization and conduction. QRS prolongation has been associated with poor heart failure prognosis and cardiovascular mortality, including sudden death. While previous genome-wide association studies (GWAS) have identified 32 QRS SNPs across 26 loci among European, African, and Asian-descent populations, the genetics of QRS among Hispanics/Latinos has not been previously explored.

Methods

We performed a GWAS of QRS duration among Hispanic/Latino ancestry populations (n=15,124) from four studies using 1000 Genomes imputed genotype data (adjusted for age, sex, global ancestry, clinical and study-specific covariates). Study-specific results were combined using fixed-effects, inverse variance-weighted meta-analysis.

Results

We identified six loci associated with QRS (P<5×10−8), including two novel loci:MYOCD, a nuclear protein expressed in the heart, andSYT1, an integral membrane protein. The top association in theMYOCDlocus, intronic SNP rs16946539, was found in Hispanics/Latinos with a minor allele frequency (MAF) of 0.04, but is monomorphic in European and African descent populations. The most significant QRS duration association was for intronic SNP rs3922344 (P= 8.56×10−26) inSCN5A/SCN10A. Three additional previously identified loci,CDKN1A,VTI1A, andHAND1, also exceeded the GWAS significance threshold among Hispanics/Latinos. A total of 27 of 32 previously identified QRS duration SNPs were shown to generalize in Hispanics/Latinos.

Conclusions

Our QRS duration GWAS, the first in Hispanic/Latino populations, identified two new loci, underscoring the utility of extending large scale genomic studies to currently under-examined populations.
New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet
Authors: Freed Nikki E. , Pearman William S. , Smith Adam N. H. , Breckell Georgia , Dale James , Silander Olin K.
Published: July 2018

Background

Using metagenomics to determine animal diet offers a new and promising alternative to current methods. Here we show that rapid and inexpensive diet quantification is possible through metagenomic sequencing with the portable Oxford Nanopore Technologies (ONT) MinION. Using an amplification-free approach, we profiled the stomach contents from wild-caught rats.

Results

We conservatively identified diet items from over 50 taxonomic orders, ranging across nine phyla that include plants, vertebrates, invertebrates, and fungi. This highlights the wide range of taxa that can be identified using this simple approach. We calibrate the accuracy of this method by comparing the characteristics of reads matching the ground-truth host genome (rat) to those matching diet items, and show that at the family-level, false positive taxon assignments are approximately 97.5% accurate. We also suggest a way to mitigate for database biases in metagenomic approaches. Finally, we implement a constrained ordination analysis and show that we can identify the sampling location of an individual rat within tens of kilometres based on diet content alone.

Conclusions

This work establishes proof-of-principle for long-read metagenomic methods in quantitative diet analysis. We show that diet content can be quantified even with limited expertise, using a simple, amplification free workflow and a relatively inexpensive and accessible next generation sequencing method. Continued increases in the accuracy and throughput of ONT sequencing, along with improved genomic databases, suggests that a metagenomic approach to quantification of animal diets will become an important method in the future.
Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat
Authors: Gardiner Laura-jayne , Brabbs Thomas , Akhunova Alina , Jordan Katherine , Budak Hikmet , Richmond Todd , Singh Sukwinder , Catchpole Leah , Akhunov Eduard , Hall Anthony
Published: July 2018

Background

Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits.

Results

We present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and promoter capture.

Conclusions

We show that a capture design employing an ‘island strategy’ can enable analysis of the large gene/promoter space of wheat with only 2×160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
Energetic substrate availability regulates synchronous activity in an excitatory neural network
Authors: Tourigny David S. , Kaiser Abdul Karim Muhammad , Echeveste Rodrigo , Kotter Mark R. N. , O’Neill John S.
Published: July 2018

Neural networks are required to meet significant metabolic demands associated with performing sophisticated computational tasks in the brain. The necessity for efficient transmission of information imposes stringent constraints on the metabolic pathways that can be used for energy generation at the synapse, and thus low availability of energetic substrates can reduce the efficacy of synaptic function. Here we study the effects of energetic substrate availability on global neural network behavior and find that glucose alone can sustain excitatory neurotransmission required to generate high-frequency synchronous bursting that emerges in culture. In contrast, obligatory oxidative energetic substrates such as lactate and pyruvate are unable to substitute for glucose, indicating that processes involving glucose metabolism form the primary energy-generating pathways supporting coordinated network activity. Our experimental results are discussed in the context of the role that metabolism plays in supporting the performance of individual synapses, including the relative contributions from postsynaptic responses, astrocytes, and presynaptic vesicle cycling. We propose a simple computational model for our excitatory cultures that accurately captures the inability of metabolically compromised synapses to sustain synchronous bursting when extracellular glucose is depleted.
Short-term radiofrequency exposure from new generation mobile phones reduces EEG alpha power with no effects on cognitive performance
Authors: Vecsei Zsuzsanna , Knakker Balázs , Juhász Péter , Thuróczy György , Trunk Attila , Hernádi István
Published: July 2018

Although mobile phone (MP) use has been steadily increasing in the last decades and similar positive trends are expected for the near future, systematic investigations on neurophysiological and cognitive effects caused by recently developed technological standards for MPs are scarcely available. Here, we investigated the effects of radiofrequency (RF) fields emitted by new-generation mobile technologies, specifically, Universal Mobile Telecommunications System (UMTS) and Long-Term Evolution (LTE), on intrinsic scalp EEG activity in the alpha band (8–12 Hz) and cognitive performance in the Stroop test. The study involved 60 healthy, young-adult university students (34 for UMTS and 26 for LTE) with double-blind administration of Real and Sham exposure in separate sessions. EEG was recorded before, during and after RF exposure, and Stroop performance was assessed before and after EEG recording. Both RF exposure types caused a notable decrease in the alpha power over the whole scalp that persisted even after the cessation of the exposure, whereas no effects were found on any aspects of performance in the Stroop test. The results imply that the brain networks underlying global alpha oscillations might require minor reconfiguration to adapt to the local biophysical changes caused by focal RF exposure mimicking MP use.
DrosophilaHox genes induce melanised pseudo-tumours when misexpressed in hemocytes
Authors: Ponrathnam Titus , Mishra Rakesh K
Published: July 2018

Homeotic genes are the key early determinants of cell identity along the anterior-posterior body axis across bilaterians. More recently, however, several late non-homeotic functions of hox genes have emerged in a variety of organogenesis processes, including in mammals. Being crucial factors in determining cell identity and organogenesis, the misregulation of hox genes is likely to be associated with defects in these processes. Several studies have reported misexpression of hox genes in a variety of malignancies including acute myeloid leukaemia. Considering thatDrosophilais a well-established model for the study of haematopoiesis, we ectopically expressed the hox genes,Dfd,Ubx,abd-AandAbd-B, to ask if and how it will alter the process of haematopoiesis. We observed black melanised spots circulating in the viscera of the larvae and extensive lethality at during the pupal stage in these conditions. Such abnormalities are the hallmark of dysregulated haematopoiesis. We also observed an increase in blood cell number as well as their enhanced differentiation into lamellocytes. Our study opens a new possibility of addressing the function hox genes in normal and leukemogenic hematopoiesis with potential implications in downstream targets for diagnostic markers and therapy.

DrosophilaHox genes, when expressed in blood cells, are leukemogenic, induce cell autonomous proliferation and differentiation. This reinforces previous studies in vertebrates and allows for Hox induced leukaemia to be studied inDrosophila.
Genome-wide maps of distal gene regulatory regions active in the human placenta
Authors: Zhang Joanna , Simonti Corinne N. , Capra John A.
Published: July 2018

Placental dysfunction is implicated in many pregnancy complications, including preeclampsia and preterm birth (PTB). While both these syndromes are influenced by environmental risk factors, they also have a substantial genetic component that is not well understood. Precisely controlled gene expression during development is crucial to proper placental function and often mediated through gene regulatory enhancers. However, we lack accurate maps of placental enhancer activity due to the challenges of assaying the placenta and the difficulty of comprehensively identifying enhancers. To address the gap in our knowledge of gene regulatory elements in the placenta, we used a two-step machine learning pipeline to synthesize existing functional genomics studies, transcription factor (TF) binding patterns, and evolutionary information to predict placental enhancers. The trained classifiers accurately distinguish enhancers from the genomic background and placental enhancers from enhancers active in other tissues. Genomic features collected from tissues and cell lines involved in pregnancy are the most predictive of placental regulatory activity. Applying the classifiers genome-wide enabled us to create a map of 33,010 predicted placental enhancers, including 4,562 high-confidence enhancer predictions. The genome-wide placental enhancers are significantly enriched nearby genes associated with placental development and birth disorders and for SNPs associated with gestational age. These genome-wide predicted placental enhancers provide candidate regions for further testing in vitro, will assist in guiding future studies of genetic associations with pregnancy phenotypes, and aid interpretation of potential mechanisms of action for variants found through genetic studies.
Evidence for a Recombinant Origin of HIV-1 group M from Genomic Variation
Authors: Olabode Abayomi S , Avino Mariano , Ng Tammy , Abu-Sardanah Faisal , Dick David W , Poon Art FY
Published: July 2018

Reconstructing the early dynamics of the HIV-1 pandemic can provide crucial insights into the socioeconomic drivers of emerging infectious diseases in human populations, including the roles of urbanization and transportation networks. Current evidence indicates that the global pandemic comprising almost entirely of HIV-1/M originated around the 1920s in central Africa. However, these estimates are based on molecular clock estimates that are assumed to apply uniformly across the virus genome. There is growing evidence that recombination has played a significant role in the early history of the HIV-1 pandemic, such that different regions of the HIV-1 genome have different evolutionary histories. In this study, we have conducted a dated-tip analysis of all near full-length HIV-1/M genome sequences that were published in the GenBank database. We used a sliding window approach similar to the ‘bootscanning’ method for detecting breakpoints in intersubtype recombinant sequences. We found evidence of substantial variation in estimated root dates among windows, with an estimated mean time to the most recent common ancestor (tMRCA) of 1922. Estimates were significantly autocorrelated, which was more consistent with an early recombination event than with stochastic error variation in phylogenetic reconstruction and dating analyses. A piecewise regression analysis supported the existence of at least one recombination breakpoint in the HIV-1/M genome with interval-specific means around 1929 and 1913, respectively. This analysis demonstrates that a sliding window approach can accommodate early recombination events outside the established nomenclature of HIV-1/M subtypes, although it is difficult to incorporate the earliest available samples due to their limited genome coverage.
Latitudinal Variation in Life History Reveals a Reproductive Disadvantage in the Texas Horned Lizard (Phrynosoma cornutum)
Authors: Hughes Daniel F. , Meshaka Walter E. , Lieb Carl S. , Pechmann Joseph H. K.
Published: July 2018

Geographically widespread species that occupy many thermal environments provide testable models for understanding the evolution of life-history responses to latitude, yet studies that draw range-wide conclusions using descriptive data from populations in the core of a species’ distribution can overlook meaningful inter-population variation. The phrynosomatid lizardPhrynosoma cornutumspans an extensive latitudinal distribution in North America and has been well-studied in connection with life-history evolution, yet populations occupying the most northern and coldest areas within its range were absent from previous examinations. We tested genus-wide models and challenged species-specific findings on the evolution of the life-history strategy forP. cornutumusing populations at the northern edge of its geographic range and comparative material from farther south. Multivariate analyses revealed that egg dimensions decreased with clutch size, suggestive of a previously unrecognized tradeoff between egg size and egg number in this species. Interestingly, reproductive traits of females with shelled eggs did not covary with latitude, yet we found that populations at the highest latitudes typified several traits of the genus and for the species, including a model forPhrynosomaof large clutches and delayed reproduction. A significant deviation from earlier findings is that we detected latitudinal variation in clutch size. This finding, although novel, is unsurprising given the smaller body sizes from northern populations and the positive relationship between clutch size and body size. Intriguing, however, was that the significant reduction in clutch size persisted when female body size was held constant, indicating a reproductive disadvantage to living at higher latitudes. We discuss the possible selective pressures that may have resulted in the diminishing returns on reproductive output at higher latitudes. Our findings highlight the type of insights in the study of life-history evolution that can be gained across Phrynosomatidae from the inclusion of populations representing latitudinal endpoints.
Covariation analysis with improved parameters reveals conservation in lncRNA structures
Authors: Tavares Rafael C A , Pyle Anna Marie , Somarowthu Srinivas
Published: July 2018

The existence of phylogenetic covariation in base-pairing is strong evidence for functional elements of RNA structure, although available tools for identifying covariation are limited. R-scape is a recently developed program for prediction of covariation from sequence alignments, but it has limited utility on long RNAs, especially those of eukaryotic origin. Here we show that R-scape can be adapted for powerful prediction of covariation in long RNA molecules, including mammalian lncRNAs.
Construction of a three-dimensional supramolecular framework based on an anionic cadmium(II) coordination network and protonated dipyridine organic cations
Authors: Zhou Qian-Kun , Wang Lin , Liu Dong
Published: July 2018

As a class of multifunctional materials, crystalline supramolecular complexes have attracted much attention because of their unique architectures, intriguing topologies and potential applications. In this article, a new supramolecular compound, namely catena-poly[4,4′-(buta-1,3-diene-1,4-diyl)dipyridin-1-ium [(μ4-benzene-1,2,4,5-tetracarboxylato-κ6
O
1,O
1′:O
2:O
4,O
4′:O
5)cadmium(II)]], {(C14H14N2)[Cd(C10H2O8)]}
n
or {(1,4-H2bpbd)[Cd(1,2,4,5-btc)]}
n
, has been prepared by the self-assembly of Cd(NO3)2·4H2O, benzene-1,2,4,5-tetracarboxylic acid (1,2,4,5-H4btc) and 1,4-bis(pyridin-4-yl)buta-1,3-diene (1,4-bpbd) under hydrothermal conditions. The title compound has been structurally characterized by IR spectroscopy, elemental analysis, powder X-ray diffraction and single-crystal X-ray diffraction analysis. Each CdII centre is coordinated by six O atoms from four different (1,2,4,5-btc)4− tetraanions. Each CdII cation, located on a site of twofold symmetry, binds to four carboxylate groups belonging to four separate (1,2,4,5-btc)4− ligands. Each (1,2,4,5-btc)4− anion, situated on a position of \overline{1} symmetry, binds to four crystallographically equivalent CdII centres. Neighbouring CdII cations interconnect bridging (1,2,4,5-btc)4− anions to form a three-dimensional {[Cd(1,2,4,5-btc)]2−}
n
anionic coordination network with infinite tubular channels. The channels are visible in both the [1\overline{1}0] and the [001] direction. Such a coordination network can be simplified as a (4,4)-connected framework with the point symbol (4284)(4284). To balance the negative charge of the metal–carboxylate coordination network, the cavities of the network are occupied by protonated (1,4-H2bpbd)2+ cations that are located on sites of twofold symmetry. In the crystal, there are strong hydrogen-bonding interactions between the anionic coordination network and the (1,4-H2bpbd)2+ cations. Considering the hydrogen-bonding interactions, the structure can be further regarded as a three-dimensional (4,6)-connected supramolecular architecture with the point symbol (4264)(42687·84). The thermal stability and photoluminescence properties of the title compound have been investigated.
Crystal structure of 3,14-dimethyl-2,6,13,17-tetraazoniatricyclo[16.4.0.07,12]docosane tetrachloride tetrahydrate from synchrotron X-ray data
Authors: Moon Dohyun , Choi Jong-Ha
Published: July 2018

The crystal structure of the title salt, C20H44N4
4+·4Cl−·4H2O, has been determined using synchrotron radiation at 220 K. The structure determination reveals that protonation has occurred at all four amine N atoms. The asymmetric unit contains one half-cation (completed by crystallographic inversion symmetry), two chloride anions and two water molecules. There are two molecules in the unit cell. The Cl− anions and hydrate molecules are involved in hydrogen bonding. The crystal structure is stabilized by intermolecular hydrogen bonds involving the macrocycle N—H groups and water O—H groups as donors and the O atoms of the water molecules and the Cl− anions as acceptors, giving rise to a three-dimensional network.
Strategies to manage hail risk in apple production
Authors: Porsch Annkatrin , Gandorfer Markus , Bitsch Vera
Published: July 2018

Purpose

Hail risk management is essential for successful farm management in German fruit production, particularly because hail events and associated losses have increased in recent years. The purpose of this paper is to conduct a detailed risk analysis comparing different strategies to manage hail risk, taking into account farmers’ risk aversion and farm-specific conditions.

Design/methodology/approach

Within an expected utility framework, two different strategies for managing hail risk are compared: one belonging to the group of financial instruments (hail insurance) and the other to the group of technical instruments (anti-hail net). A unique data set comprising a ten-year time series of orchard-specific hail damage and hail insurance data is used.

Findings

For orchards with low local hail risk and low yield potential, not using hail risk mitigation is most efficient. For orchards with high local hail risk and high yield potential, anti-hail nets provide the highest certainty equivalents. For orchards with high local risk, but low yield potential, hail insurance is most efficient. For orchards, with low local risk, but high yield potential, the certainty equivalents are higher for anti-hail net, when the farmer is risk neutral or slightly risk-averse. With increasing risk aversion, hail insurance is most efficient, which can be explained by the greater degree of the instrument’s flexibility.

Originality/value

The novelty of the study lies in the direct comparison of the risk effects of anti-hail nets and hail insurance in fruit production.
Linking protean and boundaryless career with organizational commitment
Authors: Alonderienė Raimonda , Šimkevičiūtė Indrė
Published: July 2018

Purpose

Due to the changes in the market, the shift to proactive and self-developed career management is evident. It results in the emergence of contemporary career attitudes, namely, protean and boundaryless ones. Individuals with protean career (PC) and boundaryless career (BC) attitudes may be more inclined to switch jobs, which affect decreased organizational commitment. The purpose of this paper is to analyze whether PC and BC attitudes affect organizational commitment of young adults in finance sector.

Design/methodology/approach

The data of 177 young Lithuanian adults from finance sector were collected in quantitative research.

Findings

The research results indicate that young adults in finance sector have contemporary career attitudes significantly expressed. The regression analysis findings show that affective commitment is positively predicted by self-directed career management and boundaryless mindset, and negatively predicted by values-driven career orientation and organizational mobility preference. Continuance commitment is negatively predicted by self-directed career management and organizational mobility preference.

Originality/value

This research is valuable as few if any studies cover contemporary career attitudes and organizational commitment of already working young adults in finance sector in a European country, namely, Lithuania.