bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
Authors: Badet Thomas , Oggenfuss Ursula , Abraham Leen , McDonald Bruce A. , Croll Daniel 
Published: October 2019

AbstractBackgroundThe gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures.ResultsHere, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ∼60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable elements content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species.ConclusionsTaken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
Identification of a core module for bone mineral density through the integration of a co-expression network and GWAS data
Authors: Sabik Olivia L , Calabrese Gina M , Taleghani Eric , Ackert-Bicknell Cheryl L , Farber Charles R 
Published: October 2019

AbstractRecently, the “omnigenic” model of the genetic architecture of complex traits proposed two general categories of causal genes, core and peripheral. Core genes are hypothesized to play a direct role in regulating disease; thus, their identification has the potential to reveal critical regulators and novel therapeutic targets. Here, we sought to identify genes with “core-like” characteristics for bone mineral density (BMD), one of the most significant predictors of osteoporotic fracture. This was accomplished by analyzing genome-wide association study (GWAS) data through the lens of a cell-type and timepoint-specific gene co-expression network for mineralizing osteoblasts. We identified a single co-expression network module that was enriched for genes implicated by GWAS and partitioned BMD heritability, correlated with in vitro osteoblast mineralization, and enriched for genes, which when mutated in humans or mice, led to a skeletal phenotype. Further characterization of this module identified four novel genes (B4GALNT3, CADM1, DOCK9, and GPR133) located within BMD GWAS loci with colocalizing expression quantitative trait loci (eQTL) and altered BMD in mouse knockouts, suggesting they are causal genetic drivers of BMD in humans. Our network-based approach identified a “core” module for BMD and provides a resource for expanding our understanding of the genetics of bone mass.
Robust Estimation of Bacterial Cell Count from Optical Density
Authors: Beal Jacob , Farny Natalie G. , Haddock-Angelli Traci , Selvarajah Vinoo , Baldwin Geoff S. , Buckley-Taylor Russell , Gershater Markus , Kiga Daisuke , Marken John , Sanchania Vishal , Sison Abigail , Workman Christopher T. ,   the iGEM Interlab Study Contributors
Published: October 2019

AbstractOptical density (OD) is a fast, cheap, and high-throughput measurement widely used to estimate the density of cells in liquid culture. These measurements, however, cannot be compared between instruments without a standardized calibration protocol and are challenging to relate to actual cell count. We address these shortcomings with an interlaboratory study comparing three OD calibration protocols, as applied to eight strains of E. coli engineered to constitutively express varying levels of GFP. These three protocols—comparison with colloidal silica (LUDOX), serial dilution of silica microspheres, and a reference colony-forming unit (CFU) assay—are all simple, low-cost, and highly accessible. Based on the results produced by the 244 teams completing this interlaboratory study, we recommend calibrating OD using serial dilution of silica microspheres, which readily produces highly precise calibration (95.5% of teams having residuals less than 1.2-fold), is easily assessed for quality control, and as a side effect also assesses the effective linear range of an instrument. Moreover, estimates of cell count from silica microspheres can be combined with fluorescence calibration against fluorescein to obtain units of Molecules of Equivalent Fluorescein (MEFL), allowing direct comparison and data fusion with equivalently calibrated flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
Significant improvement of reprogramming efficiency by transient overexpression of ZGA inducer Dux but not Dppa2/4
Authors: Yang Lei , Liu Xuefei , Song Lishuang , Di Anqi , Su Guanghua , Bai Chunling , Wei Zhuying , Li Guangpeng 
Published: October 2019

AbstractCloned animal have been reported by somatic cell nuclear transfer (SCNT) for many years. However, the SCNT is extremely inefficient, and zygotic genome activation (ZGA) is required for SCNT and chemical mediated reprogramming. To identify candidate factors that facilitate ZGA in reprogramming, we performed siRNA-repressor and mRNA-inducer screening, which revealed Dux, Dppa2, and Dppa4 as key factors enhancing the ZGA in SCNT. Direct injection of ZGA-inducers had no significant effect on the SCNT blastocyst formation, and even destroyed the ZGA. Through a inducible Dux transgenic mouse model, we demonstrate that transient overexpression of Dux not only improved SCNT efficiency, but also increased the efficiency of chemical reprogramming. Transcriptome profiling revealed that Dux treated SCNT embryos were similar to fertilized embryos. Furthermore, transient overexpression of Dux combined with inactivation of DNA methyltransferases (Dnmts) further promote the overall development of SCNT-derived animals. These findings enhance our understanding of ZGA-regulators in somatic reprogramming.
Oscillation-driven memory encoding, maintenance and recall in an entorhinal-hippocampal circuit model
Authors: Kurikawa Tomoki , Mizuseki Kenji , Fukai Tomoki 
Published: October 2019

SummaryDuring the execution of working memory tasks, task-relevant information is processed by local circuits across multiple brain regions. How this multi-area computation is conducted by the brain remains largely unknown. To explore such mechanisms in spatial working memory, we constructed a neural network model involving parvalbumin-positive, somatostatin-positive and vasoactive intestinal polypeptide-positive interneurons in the hippocampal CA1 and the superficial and deep layers of medial entorhinal cortex (MEC). Our model is based on a hypothesis that cholinergic modulations differently regulate information flows across CA1 and MEC at memory encoding, maintenance and recall during delayed nonmatching-to-place tasks. In the model, theta oscillation coordinates the proper timing of interactions between these regions. Furthermore, the model predicts that MEC is engaged in decoding as well as encoding spatial memory, which we confirmed by experimental data analysis. Thus, our model accounts for the neurobiological characteristics of the cross-area information routing underlying working memory tasks.
Evolutionary regain of lost gene circuit function
Authors: Gouda Mirna Kheir , Manhart Michael , Balázsi Gábor 
Published: October 2019

ABSTRACTEvolutionary reversibility - the ability to regain a lost function - is an important problem both in evolutionary and synthetic biology, where repairing natural or synthetic systems broken by evolutionary processes may be valuable. Here, we use a synthetic positive-feedback (PF) gene circuit integrated into haploidSaccharomyces cerevisiaecells to test if the population can restore lost PF function. In previous evolution experiments, mutations in a gene eliminated the fitness costs of PF activation. Since PF activation also provides drug resistance, exposing such compromised or broken mutants to both drug and inducer should create selection pressure to regain drug resistance and possibly PF function. Indeed, evolving seven PF mutant strains in the presence of drug revealed three adaptation scenarios through genomic mutations outside of the PF circuit that elevate PF basal expression, possibly by affecting transcription, translation, degradation and other fundamental cell functions. Nonfunctional mutants gained drug resistance without ever developing high expression, while quasi-functional and dysfunctional PF mutants developed high expression which then diminished, although more slowly for dysfunctional mutants where revertant clones arose. These results highlight how intracellular context, such as the growth rate, can affect regulatory network dynamics and evolutionary dynamics, which has important consequences for understanding the evolution of drug resistance and developing future synthetic biology applications.Significance StatementNatural or synthetic genetic modules can lose their function over long-term evolution if the function is costly. How populations can evolve to restore broken functions is poorly understood. To test the reversibility of evolutionary breakdown, we use yeast cell populations with a chromosomally integrated synthetic gene circuit. In previous evolution experiments the gene circuit lost its costly function through various mutations. By exposing such mutant populations to conditions where regaining gene circuit function would be beneficial we find adaptation scenarios with or without repairing lost gene circuit function. These results are important for drug resistance or future synthetic biology applications where loss and regain of function play a significant role.
A Mechanical Model of Early Somite Segmentation
Authors: Adhyapok Priyom , Piatkowska Agnieszka M , Norman Michael J , Clendenon Sherry G , Stern Claudio D , Glazier James A , Belmonte Julio M 
Published: October 2019

AbstractThe clock-and-wavefront model (CW) hypothesizes that the formation of somites in vertebrate embryos results from the interplay of molecular oscillations with a wave traveling along the body axis. This model however does not explain how molecular information is interpreted by cells to modulate their rearrangement into somites. Here we performed Scanning Electron Microscopy (SEM) on the pre-somitic mesoderm (PSM) of chicken embryos at stages 11-12 to describe in detail the cell shape changes occurring along the axis of the PSM. This reveals a wave of epithelialization of the dorsal PSM that precedes somite segmentation. Signs of spatially periodic apical constriction appear in this layer starting at least 3-4 somite lengths caudal to the most recently formed somite. The sizes of these clusters correspond to the typical diameter of chicken somites. We propose that a mechanical instability process leads to the separation of cells into these structures and positions the future inter-somite boundaries. We present a model in which a wave of apical constriction leads to increasing tension and periodic failure of adhesion junctions within the dorsal epithelial layer of the PSM, thus positioning somite boundaries. This model can produce spatially periodic segments whose size depends on the speed of the contraction wave (W) and the rate of increase of apical contractility (Λ). The Λ/W ratio determines whether this mechanism produces spatially and temporally regular or irregular segments, and whether segment sizes increase with the wave speed (scaling) as in the CW model. We discuss the limitations of a purely mechanical model of somite segmentation and the role of biomechanics along with CW during somitogenesis.
From aura to jargon: the social life of authentication
Authors: Södergren Jonatan 
Published: October 2019

PurposeAuthenticity has emerged as a prevailing purchase criterion that seems to include both real and stylised versions of the truth. The purpose of this paper is to address the negotiation of authenticity by examining the means by which costume designers draw on cues such as historical correctness and imagination to authenticate re-enactments of historical epochs in cinematic artwork.Design/methodology/approachTo understand and analyse how different epochs were re-enacted required interviewing costume designers who have brought reimagined epochs into being. The questions were aimed towards acknowledging the socio-cultural circulation of images that practitioners draw from in order to project authenticity. This study was conducted during a seven-week internship at a costume store called Independent Costume in Stockholm as part of a doctoral course in cultural production.FindingsAuthenticity could be found in citations that neither had nor resembled something with an indexical link to the original referent as long as the audience could make a connection to the historical epoch sought to re-enact. As such, it would seem that imagination and historical correctness interplay in impressions of authenticity. Findings suggest that performances of authentication are influenced by socially instituted discursive practices (i.e. jargons) and collective imagination.Originality/valueThis paper contributes to the literature on social and performative aspects of authentication as well as its implications for brands in the arts and culture sector.
How website browsing impacts expectations of store features
Authors: Loupiac Philippine , Goudey Alain 
Published: October 2019

Purpose
E-commerce has become a key component of brand retail strategies since the advent of omni-channel distributions. Many researchers have investigated the strategic role of e-commerce, and some recent articles show the importance of exploring the impact of this distribution model on consumer behaviour. However, there is no study focusing on how visits to a website create expectations of the shop. Relying on the expectancy-value theory and the omni-channel literature, the purpose of this paper is to fill this gap by focusing on how the digital channel can create expectations for the physical channel.

Design/methodology/approach
This study is based on 24 semi-directive interviews with consumers, and all interviews included a browsing session on a real website. The methodology consists of both a thematic analysis of the interviews and a lexicographic analysis of the verbatim.

Findings
The findings reveal that direct online experience on a website will create beliefs about the physical stores of the same brand. These beliefs will, in turn, influence consumer attitudes towards the store. The study is the first to highlight such a link between channels and to explain in detail how this relationship arises.

Originality/value
The main contribution of this work includes showing the existence of a strong link between web-based and physical retail. From a managerial perspective, the study suggests that, from an omni-channel perspective, the design of the website impacts expectations towards the physical store in terms of its atmosphere, its location, its merchandising and even its level of crowding.
Exploring the effect of internal and external integration on the performance of professional service outsourcing
Authors: Liu Zuoming , Jayaraman Vaidyanathan 
Published: October 2019

PurposeThis paper aims to investigate how the professional service outsourcing (PSO) firm’s external knowledge integration with global clients, internal integration across various functional units and the synergistic effects between them in improving PSO performance.Design/methodology/approachDrawing on the theory of organizational learning, a conceptual framework is proposed with hypothesized relationships. The relationships in this conceptual model were tested using a structural equation model (SEM) to analyze a survey dataset including 192 Indian-based professional service providers.FindingsA service provider’s performance is positively associated with its external integration with global clients and internal integration across various functional units. Synergistic effect is generated from balanced high-level external and internal integration in improving PSO performance.Research limitations/implicationsThis study contributes to the much-needed efforts in studying PSO, a new and fast-growing cross-border professional service activity, and provides helpful managerial implications to practicing global clients and offshore PSO service providers on how to successfully manage and govern the outsourcing process to achieve expected benefits.Originality/valueThis study focuses on offshore service provider’s viewpoint to extend traditional supply-chain integration regarding cooperative and mutually beneficial mechanisms to the context of PSO.
Excess body weight and abdominal obesity in relation to selected psychosocial characteristics in primary school children
Authors: Vassiloudis Ioannis , Costarelli Vassiliki 
Published: October 2019

PurposeThe purpose of this paper is to investigate excess body weight and abdominal obesity in relation to selected psychosocial characteristics such as self-perception, self-esteem and anxiety, in primary school children.Design/methodology/approachA school-based cross-sectional study was conducted with a total of 528 students 10-12 years of age, randomly selected, from the area of Athens, Greece. The Greek versions of the self-perception profile for children (SPPC) and the state-trait anxiety inventory for children (STAI-C) questionnaires have been used to determine the children’s self-perception/self-esteem and the status of anxiety, respectively. Standard anthropometric measurements were also taken. Pearson correlation coefficient was used to test for possible linear correlations between data variables. One-way ANOVA and independentt-test were used to determine statistically significant differences between the means of children’s body mass index (BMI) – abdominal obesity groups. For multiple comparisons, Bonferroni post-tests were run.FindingsOverweight and obese children and children with abdominal obesity had lower scores in all of the domains of SPPC self-perception, the SPPC global self-esteem and the STAI-C anxiety levels in comparison to normal weight children. BMI and abdominal obesity correlated negatively with each one of the five domains of the SPPC self-perception (p < 0.001) and the SPPC global self-esteem (p < 0.001) and positively with the STAI-C anxiety levels (p < 0.005). One-way ANOVA and independentt-test revealed statistically significant differences between the means of children’s BMI and abdominal obesity groups in all the domains of SPPC self-perception (p < 0.001), the SPPC global self-esteem (p < 0.001) and the STAI-C anxiety levels (p < 0.005). There were no gender differences in the psychometric characteristics assessed in this study.Originality/valuePrimary school children with excess body weight and abdominal obesity have increased anxiety levels and they score lower in key psychosocial characteristics, in comparison to normal weight children.
Buying a family car: relevant factors for teenagers
Authors: de Sa Joao Duarte Saleme , Mainardes Emerson Wagner , Andrade Daniel Modenesi de 
Published: October 2019

Purpose
The purpose of this paper is to find out the relevant factors, according to teenagers, that influence the buying decision of the family car.

Design/methodology/approach
Research carried out in three stages: one qualitative research (by using focal groups), and two quantitative research studies (descriptive and cross-sectional).

Findings
The authors identified three factors that are important for teenagers when influencing the purchase of the family car: safety, sportiness and comfort. The identification of these factors shows that the millennial generation tends to emphasize aspects of individual interest, such as status and performance, and family context, such as safety and comfort, rather than social aspects, such as the type of fuel and environmental impact.

Practical implications
The authors recommend the development of automobiles that prioritize the three factors mentioned herein in order to reverse the trend of declining car purchase.

Originality/value
The authors presented the relevant attributes in buying decisions of family cars according to teenagers. The authors also indicated the automobile attributes that are relevant for a more informed, connected, and with an increasing purchase power generation in contrast with previous generations, whose social context was prior to the emergence of social media.
Spatio-temporal analysis of land use changes using remote sensing in Horqin sandy land, China
Authors: Zhao Zhenzhen , Feng Jiandi 
Published: October 2019

PurposeThe purpose of this paper is to analyze the characteristics of spatio-temporal dynamics and the evolution of land use change is essential for understanding and assessing the status and transition of ecosystems. Such analysis, when applied to Horqin sandy land, can also provide basic information for appropriate decision-making.Design/methodology/approachBy integrating long time series Landsat imageries and geographic information system (GIS) technology, this paper explored the spatio-temporal dynamics and evolution-induced land use change of the largest sandy land in China from 1983 to 2016. Accurate and consistent land use information and land use change information was first extracted by using the maximum likelihood classifier and the post-classification change detection method, respectively. The spatio-temporal dynamics and evolution were then analyzed using three kinds of index models: the dynamic degree model to analyze the change of regional land resources, the dynamic change transfer matrix and flow direction rate to analyze the change direction, and the barycenter transfer model to analyze the spatial pattern of land use change.FindingsThe results indicated that land use in Horqin sandy land during the study period changed dramatically. Vegetation and sandy land showed fluctuating changes, cropland and construction land steadily increased, water body decreased continuously, and the spatial distribution patterns of land use were generally unbalanced. Vegetation, sandy land and cropland were transferred frequently. The amount of vegetation loss was the largest. Water body loss was 473.6 km2, which accounted for 41.7 per cent of the total water body. The loss amount of construction land was only 1.0 km2. Considerable differences were noted in the rate of gravity center migration among the land use types in different periods, and the overall rate of construction land migration was the smallest. Moreover, the gravity center migration rates of the water body and sandy land were relatively high and were related to the fragile ecological environment of Horqin sandy land.Originality/valueThe results not only confirmed the applicability and effectiveness of the combined method of remote sensing and GIS technology but also revealed notable spatio-temporal dynamics and evolution-induced land use change throughout the different time periods (1983-1990, 1990-2000, 2000-2010, 2010-2014, 2014-2016 and 1983-2016).