bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue
Authors: Liu Yang , Yang Mingyu , Deng Yanxiang , Su Graham , Enninful Archibald , Guo Cindy C. , Tebaldi Toma , Zhang Di , Kim Dongjoo , Bai Zhiliang , Norris Eileen , Pan Alisia , Li Jiatong , Xiao Yang , Halene Stephanie , Fan Rong 
Published: October 2019

SUMMARYWe present DBiT-seq –Deterministic Barcoding in Tissue for spatial omics sequencing – for co-mapping of mRNAs and proteins in a formaldehyde-fixed tissue slide via NGS sequencing. Parallel microfluidic channels were used to deliver DNA barcodes to the surface of a tissue slide and crossflow of two sets of barcodes A1-50 and B1-50 followed by ligationin situyielded a 2D mosaic of tissue pixels, each containing a unique full barcode AB. Application to mouse embryos revealed major tissue types in early organogenesis as well as fine features like microvasculature in a brain and pigmented epithelium in an eye field. Gene expression profiles in 10μm pixels conformed into the clusters of single-cell transcriptomes, allowing for rapid identification of cell types and spatial distributions. DBiT-seq can be adopted by researchers with no experience in microfluidics and may find applications in a range of fields including developmental biology, cancer biology, neuroscience, and clinical pathology.In BriefMicrofluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high-throughput sequencing enables the construction of a high-spatial-resolution multi-omics atlas at the genome scale. Application to mouse embryos (E10-12) identified major tissue types in early organogenesis and revealed fine tissue features such as retinal pigmented epithelium and endothelial microvasculature at the cellular level.HighlightsDeterministic barcoding in tissue enables NGS-based spatial multi-omics mapping.DBiT-seq identified spatial patterning of major tissue types in mouse embryos.DBiT-seq revealed fine features such as retinal pigmented epithelium and microvascular endothelium at the cellular level.Direct integration with scRNA-seq data allows for rapid cell type identification.
Phylogeny and Multiple Independent Whole-Genome Duplication Events in the Brassicales
Authors: Mabry Makenzie E. , Brose Julia M. , Blischak Paul D. , Sutherland Brittany , Dismukes Wade T. , Bottoms Christopher A. , Edger Patrick P. , Washburn Jacob D. , An Hong , Hall Jocelyn C. , McKain Michael R. , Al-Shehbaz Ihsan , Barker Michael S. , Schranz M. Eric , Conant Gavin C. , Pires J. Chris 
Published: October 2019

ABSTRACTWhole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. However, while its sister family, Cleomaceae, has also been characterized by a WGD, its placement, as well as that of other WGD events in other families in the order, remains unclear. Using phylo-transcriptomics from 74 taxa and genome survey sequencing for 66 of those taxa, we infer nuclear and chloroplast phylogenies to assess relationships among the major families of the Brassicales and within the Brassicaceae. We then use multiple methods of WGD inference to assess placement of WGD events. We not only present well-supported chloroplast and nuclear phylogenies for the Brassicales, but we also putatively place Th-α and provide evidence for previously unknown events, including one shared by at least two members of the Resedaceae, which we name Rs-α. Given its economic importance and many genomic resources, the Brassicales are an ideal group to continue assessing WGD inference methods. We add to the current conversation on WGD inference difficulties, by demonstrating that sampling is especially important for WGD identification.
Population specific reference panels are crucial for the genetic analyses of Native Hawai’ians: an example of theCREBRFlocus
Authors: Lin Meng , Caberto Christian , Wan Peggy , Li Yuqing , Lum-Jones Annette , Tiirikainen Maarit , Pooler Loreall , Nakamura Brooke , Sheng Xin , Porcel Jacqueline , Lim Unhee , Setiawan Veronica Wendy , Marchand Loïc Le , Wilkens Lynne R. , Haiman Christopher A. , Cheng Iona , Chiang Charleston W. K. 
Published: October 2019

AbstractStatistical imputation applied to genome-wide array data is the most cost-effective approach to complete the catalog of genetic variation in a study population. However, imputed genotypes in underrepresented populations incur greater inaccuracies due to ascertainment bias and a lack of representation among reference individuals,, further contributing to the obstacles to study these populations. Here we examined the consequences due to the lack of representation by genotyping a functionally important, Polynesian-specific variant, rs373863828, in theCREBRFgene, in a large number of self-reported Native Hawai’ians (N=3,693) from the Multiethnic Cohort. We found the derived allele of rs373863828 was significantly associated with several adiposity traits with large effects (e.g.0.214 s.d., or approximately 1.28 kg/m2, per allele, in BMI as the most significant; P = 7.5×10−5). Due to the current absence of Polynesian representation in publicly accessible reference sequences, rs373863828 or any of its proxies could not be tested through imputation using these existing resources. Moreover, the association signals at this Polynesian-specific variant could not be captured by alternative approaches, such as admixture mapping. In contrast, highly accurate imputation can be achieved even if a small number (<200) of Polynesian reference individuals were available. By constructing an internal set of Polynesian reference individuals, we were able to increase sample size for analysis up to 3,936 individuals, and improved the statistical evidence of association (e.g. p = 1.5×10−7, 3×10−6, and 1.4×10−4for BMI, hip circumference, and T2D, respectively). Taken together, our results suggest the alarming possibility that lack of representation in reference panels would inhibit discovery of functionally important, population-specific loci such asCREBRF. Yet, they could be easily detected and prioritized with improved representation of diverse populations in sequencing studies.
A tissue-specific collaborative mixed model for jointly analyzing multiple tissues in transcriptome-wide association studies
Authors: Shi Xingjie , Chai Xiaoran , Yang Yi , Cheng Qing , Jiao Yuling , Huang Jian , Yang Can , Liu Jin 
Published: October 2019

AbstractTranscriptome-wide association studies (TWAS) integrate expression quantitative trait loci (eQTLs) studies with genome-wide association studies (GWASs) to prioritize candidate target genes for complex traits. Several statistical methods have been recently proposed to improve the performance of TWAS in gene prioritization by integrating the expression regulatory information imputed from multiple tissues, and made significant achievements in improving the ability to detect gene-trait associations. The major limitation of these methods is that they cannot be used to elucidate the specific functional effects of candidate genes across different tissues. Here, we propose a tissue-specific collaborative mixed model (TisCoMM) for TWAS, leveraging the co-regulation of genetic variations across different tissues explicitly via a unified probabilistic model. TisCoMM not only performs hypothesis testing to prioritize gene-trait associations, but also detects the tissue-specific role of candidate target genes in complex traits. To make use of widely available GWAS summary statistics, we extend TisCoMM to use summary-level data, namely, TisCoMM-S2. Using extensive simulation studies, we show that type I error is controlled at the nominal level, the statistical power of identifying associated genes is greatly improved, and false positive rate (FPR) for non-causal tissues is well controlled at decent levels. We further illustrate the benefits of our methods in applications to summary-level GWAS data of 33 complex traits. Notably, apart from better identifying potential trait-associated genes, we can elucidate the tissue-specific role of candidate target genes. The follow-up pathway analysis from tissue-specific genes for asthma shows that the immune system plays an essential function for asthma development in both thyroid and lung tissues.
CDK-regulated phase separation seeded by histone genes ensures precise growth and function of Histone Locus Bodies
Authors: Hur Woonyung , Tarzia Marco , Deneke Victoria E. , Terzo Esteban A. , Duronio Robert J. , Talia Stefano Di 
Published: October 2019

SummaryMany membrane-less organelles form through liquid-liquid phase separation, but how their size is controlled and whether size is linked to function remain poorly understood. The Histone Locus Body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of histone mRNAs. Here, we show thatDrosophilaHLBs form through phase separation of the scaffold protein multi-sex combs (Mxc). The size of HLBs is controlled in a precise and dynamic manner that is dependent on the cell cycle and zygotic gene activation. Control of HLB growth is achieved by a mechanism integrating nascent mRNAs at the histone locus, which catalyzes phase separation, and the nuclear concentration of Mxc, which is controlled by the activity of cyclin-dependent kinases. Reduced Cdk2 activity results in smaller HLBs and the appearance of nascent, misprocessed histone mRNAs. Our experiments thus identify a mechanism linking nuclear body growth and size with gene expression.
Prevalence of RFC1-Mediated Spinocerebellar Ataxia in a United States Ataxia Cohort
Authors: Syriani Dona Aboud , Wong Darice , De Gusmao Claudio M. , Andani Sameer , Mao Yuanming , Glotzer Giacomo , Lockhart Paul J. , Hassin-Baer Sharon , Khurana Vikram , Das Soma , Gomez Christopher M. , Perlman Susan , Fogel Brent L. 
Published: October 2019

ABSTRACTObjectiveRepeat expansions in RFC1 and DAB1 have recently been identified as causing cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) and spinocerebellar ataxia 37 (SCA37), respectively. We evaluated the prevalence of these repeat-expansions in an undiagnosed ataxia cohort from the United States.MethodsA cohort of 596 patients with undiagnosed familial or sporadic cerebellar ataxia were evaluated at a tertiary referral ataxia center and excluded for common genetic causes of cerebellar ataxia. Patients were then screened for the presence of pathogenic repeat expansions in RFC1 (AAGGG) and DAB1 (ATTTC) using fluorescent repeat primed polymerase chain reaction (RP-PCR). Two additional undiagnosed ataxia cohorts from different centers, totaling 96 and 13 patients respectively, were subsequently screened for RFC1 resulting in a combined 705 subjects tested.ResultsIn the initial cohort, 42 samples were identified with one expanded allele in the RFC1 gene (7.0%), and 9 had two expanded alleles (1.5%). For the additional cohorts, we found 12 heterozygous samples (12.5%) and 7 biallelic samples (7.3%) in the larger cohort, and 1 heterozygous sample (7.7%) and 3 biallelic samples (23%) in the second. In total, 19 patients were identified with biallelic repeat expansions in RFC1 (2.7%). Of these 19 patients, 6 (32%) had a clinical diagnosis of CANVAS, 10 had cerebellar ataxia with neuropathy (53%), and 3 had spinocerebellar ataxia (16%). No patients were identified with expansions in the DAB1 gene.ConclusionIn a large undiagnosed ataxia cohort from the United States, biallelic pathogenic repeat expansion in RFC1 was observed in 2.7%. Testing should be strongly considered in ataxia patients, especially those with CANVAS or neuropathy.
Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology
Authors: Wu Sean L. , Sanchez C. Hector M. , Henry John M. , Citron Daniel T. , Zhang Qian , Compton Kelly , Liang Biyonka , Verma Amit , Cummings Derek A.T. , Le Menach Arnaud , Scott Thomas W. , Wilson Anne L. , Lindsay Steven W. , Moyes Catherine L. , Hancock Penny A. , Russell Tanya L. , Burkot Thomas R. , Marshall John M. , Kiware Samson , Reiner Robert C. , Smith David L. 
Published: October 2019

AbstractMosquitoes are important vectors for pathogens of humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new approach. Unlike most previous models, this framework considers the behavioral states and state transitions of adult mosquitoes through a sequence of activity bouts. We developed a new framework for individual-based simulation models called MBITES (Mosquito Bout-based and Individual-based Transmission Ecology Simulator). In MBITES, it is possible to build models that simulate the behavior and ecology of adult mosquitoes in exquisite detail on complex resource landscapes generated by spatial point processes. We also developed an ordinary differential equation model which is the Kolmogorov forward equations for models developed in MBITES under a specific set of simplifying assumptions. While infection of the mosquito and pathogen development are one possible part of a mosquito’s state, that is not the main focus. Using extensive simulation using some models developed in MBITES, we show that vectorial capacity can be understood as an emergent property of simple behavioral algorithms interacting with complex resource landscapes, and that relative density or sparsity of resources and the need to search can have profound consequences for mosquito populations’ capacity to transmit pathogens.
Label-free characterization of visual cortical areas in awake mice via three-photon microscopy reveals correlations between functional maps and structural substrates
Authors: Yildirim Murat , Hu Ming , So Peter T. C. , Sur Mriganka 
Published: October 2019

AbstractOur understanding of the relationship between the structure and function of the intact brain is mainly shaped by magnetic resonance imaging. However, high resolution and deep-tissue imaging modalities are required to capture the subcellular relationship between structure and function, particularly in awake conditions. Here, we utilized a custom-made three-photon microscope to perform label-free third-harmonic generation (THG) microscopy as well as laser ablation to calculate effective attenuation lengths (EAL) of primary visual cortex and five adjacent visual cortical areas in awake mice. We identified each visual area precisely by retinotopic mapping via one-photon imaging of the calcium indicator GCaMP6s. EALs measured by depth-resolved THG microscopy in the cortex and white matter showed correspondence with the functional retinotopic sign map of each cortical area. To examine the basis for this correspondence, we used THG microscopy to examine several structural features of each visual area, including their cytoarchitecture, myeloarchitecture and blood vessel architecture. The cytoarchitecture of each area allowed us to estimate EAL values, which were comparable to experimental EAL values. The orientation of blood vessels and myelin fibers in the six areas were correlated with their EAL values. Ablation experiments, which provide ground truth measurements, generated 17 ± 3 % longer EALs compared to those obtained with THG imaging but were consistent with the latter. These results demonstrate a strong correlation between structural substrates of visual cortical areas, represented by EALs, and their functional visual field representation maps.
Congruity and processing fluency
Authors: Jiang Zhiying , Guan Chong , de Haaij Ivo L. 
Published: October 2019

PurposeThe purpose of this paper is to investigate the benefits of Ad-Video and Product-Video congruity for embedded online video advertising. A conceptual model is constructed to test how congruity between online advertisements, advertised products and online videos impact consumer post-viewing attitudes via processing fluency.Design/methodology/approachAn online experiment with eight versions of mock video sections (with embedded online video advertisements) was conducted. The study is a 2 (type of appeal: informational vs emotional) × 2 (Ad-Video congruity: congruent vs incongruent) × 2 (Product-Video congruity: congruent vs incongruent) full-factorial between-subject design. A total of 252 valid responses were collected for data analysis.FindingsResults show that congruity is related to the improvement of processing fluency only for informational ads/videos. The positive effect of Ad-Video congruity on processing fluency is only significant for informational appeals but not emotional appeal. Similarly, the positive effects of Product-Video congruity on processing fluency are only significant for informational appeals but not emotional appeal. Involvement has been found to be positively related to processing fluency too. Processing fluency has a positive impact on the attitudes toward the ads, advertised products and videos.Research limitations/implicationsThe finding that congruity is related to the improvement of processing fluency only for informational ads/videos extends the existing literature by identifying the type of appeal as a boundary condition.Practical implicationsBoth brand managers and online video platform owners should monitor and operationalize the content and appeal congruity, especially for informational ads on a large scale to improve consumers’ responses.Originality/valueTo the best of the authors’ knowledge, this is the first paper to examine the effects of Ad-Video and Product-Video congruity of embedded advertisements on video sharing platforms. The findings of this study add to the literature on congruity and processing fluency.
Motive and conflict in the disaster recovery process
Authors: Choi Chang Yeol , Honda Riki 
Published: October 2019

Purpose
The purpose of this study is to address the key factors for the sustainable process of long-term recovery from disaster, with focus on interdependent decisions of various players.

Design/methodology/approach
The consistency among strategies of recovery players, who make a decision based not only on direct motive but also on various complex motives and interactions with other players, is considered. Interactive decision-making during the housing reconstruction project in Sri Lanka after the 2004 Indian Ocean tsunami is analyzed using game theory.

Findings
Regarding two important decisions defining the result of recovery, players’ possible decisions are evaluated, and by using the game theoretic approach, the reasons for poor output and the conditions to shift equilibrium to that which is suitable for the long-term goal of recovery are discussed.

Originality/value
These analyses show that motive compatibility among players should be considered when we design processes for recovery from disasters.
Making dairy supply chains robust against corruption risk: a systemic exploratory study
Authors: Liu Xiaojing , Arthanari Tiru , Shi Yangyan 
Published: October 2019

PurposeTo improve robustness of a dairy supply chain (SC) against corruption, the purpose of this paper is to propose a systemic model of a corruption impacted dairy SC, exposing relationships among SC operations, risks and the impact of corruption.Design/methodology/approachCases from the dairy industry in New Zealand (NZ) are used for thematic analysis of interview data collected from participants at senior levels of NZ dairy firms. Based on these and other inputs from literature, a systemic model is built subsequently.FindingsMitigating certain risks can significantly alleviate the impact of corruption, an external factor, on supply chain performance (SCP). The causal loop diagram (CLD) developed here brings out the modifying effect of corruption on dairy risks and SCP.Practical implicationsThe illustration of the CLD helps business managers better understand the interactions among risk variables and explains the systemic reasons for SC vulnerability.Originality/valueThis is the first paper to construct a holistic system to comprehensively reveal the interactions of supply chain risks (SCRs) and the impact of corruption. Also, by utilizing SCR interactions, this study indicates a pathway to mitigate the negative effects of corruption through improving dairy SC robustness.
Impact of ownership structure and ownership concentration on credit risk of Chinese commercial banks
Authors: Liu Yang , Brahma Sanjukta , Boateng Agyenim 
Published: October 2019

Purpose
The purpose of this paper is to examine the effects of bank ownership structure and ownership concentration on credit risk.

Design/methodology/approach
Using panel data on a sample of 88 Chinese commercial banks, with 826 observations over a period of 2003–2018, this study has applied system generalised method of moments regression to examine the impact of bank ownership structure and ownership concentration on credit risk. This study has used two measures of credit risk, which are non-performing loan ratio (NPLR) and loan loss provision ratio (LLPR).

Findings
The results show that ownership type (both government and private ownership) exerts a positive and significant impact on credit risk. Measuring ownership concentration using Herfindahl–Hirchmann Index, the results indicate that concentration of ownership in the hands of government has a negative and significant effect on credit risk, whereas private ownership concentration positively impacts credit risk. Overall, the findings suggest that concentration of ownership in government hands reduces risk; however, private ownership concentration exacerbates credit risks. The results are invariant to both measures of credit risk, before and after the financial crisis.

Practical implications
The findings provide useful insight to guide policy decisions in Chinese banks’ lending policies and bank ownership.

Originality/value
Using two ex post measures of credit risk, NPLR and LLPR, and one ownership concentration measure, HHI, this study deepens our understanding on the effectiveness of Chinese banks’ corporate governance reforms on managing credit risks.
Exploring instances of deviation in joint ventures between partners’ equity share and board representation
Authors: Velez-Calle Andres 
Published: October 2019

Purpose
To date, there has been little research about the degree of correspondence between partner equity ownership and partner representation on boards of joint ventures (JVs). It is generally assumed that partners’ share equals board representation in percentage. This paper aims to explore various instances of deviation from the above norm.

Design/methodology/approach
Using a unique database of 259 JV contracts extracted from the US Securities and Exchange Commission, and by drawing from resource dependency and transaction cost theories, this manuscript explores the factors that increase or decrease the deviation between equity share and board representation.

Findings
The results show that international JVs (IJVs) tend to deviate more, while JVs with a deadlock clause, a large board and based in a stable country deviate less from the degree of correspondence between equity share and board representation.

Originality/value
This study contributes to the alliance and governance literatures by identifying factors that influence the degree of correspondence between partner investment (equity share) and control through board of director representation.