bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature accounts for the biodiversity of a hyperdiverse group of insects in urban Los Angeles
Authors: McGlynn Terrence P. , Meineke Emily K. , Bahlai Christie A. , Li Enjie , Hartop Emily A. , Adams Benjamin J. , Brown Brian V.
Published: October 2019

The urban heat island effect is a worldwide phenomenon that has been linked to species distributions and abundances in cities. However, effects of urban heat on biotic communities are nearly impossible to disentangle from effects of land cover in most cases because hotter urban sites also have less vegetation and more impervious surfaces than cooler sites within cities. We sampled phorid flies, one of the largest, most biologically diverse families of true flies (Insecta: Diptera: Phoridae), at 30 sites distributed within the central Los Angeles Basin, where we found that temperature and the density of urban land cover are decoupled. Abundance, richness, and community composition of phorids inside urban Los Angeles were most parsimoniously accounted for by mean air temperature in the week preceding sampling. Sites with intermediate mean temperatures had more phorid fly individuals and higher richness. Communities were more even at urban sites with lower minimum temperatures and sites located further away from natural areas, suggesting that communities separated from natural source populations may be more homogenized. Species composition was best explained by minimum temperature. Inasmuch as warmer areas within cities can predict future effects of climate change, phorid fly communities are likely to shift nonlinearly under future climates in more natural areas. Exhaustive surveys of biotic communities within cities, such as the one we describe here, can provide baselines for determining the effects of urban and global climate warming as they intensify.
Retinotopic-like maps of spatial sound in primary ‘visual’ cortex of blind human echolocators
Authors: Norman Liam J. , Thaler Lore
Published: October 2019

The functional specializations of cortical sensory areas were traditionally viewed as being tied to specific modalities. A radically different emerging view is that the brain is organized by task rather than sensory modality, but it has not yet been shown that this applies to primary sensory cortices. Here, we report such evidence by showing that primary ‘visual’ cortex can be adapted to map spatial locations of sound in blind humans who regularly perceive space through sound echoes. Specifically, we objectively quantify the similarity between measured stimulus maps for sound eccentricity and predicted stimulus maps for visual eccentricity in primary ‘visual’ cortex (using a probabilistic atlas based on cortical anatomy) to find that stimulus maps for sound in expert echolocators are directly comparable to those for vision in sighted people. Furthermore, the degree of this similarity is positively related with echolocation ability. We also rule out explanations based on top-down modulation of brain activity—e.g. through imagery. This result is clear evidence that task-specific organization can extend even to primary sensory cortices, and in this way is pivotal in our reinterpretation of the functional organization of the human brain.
A Personalized Multi-Component Lifestyle Intervention Program Leads to Improved Quality of Life in Persons with Chronic Kidney Disease
Authors: Headley Samuel A. , Hutchinson Jasmin C. , Thompson Brian A. , Ostroff Marissa L. , Doyle-Campbell Courtney J. , Cornelius Allen E. , Dempsey Kristen , Siddall Jennifer , Miele Emily M. , Evans Elizabeth E. , Wood Brianna , Sirois Cherilyn M. , Winston Brett A. , Whalen Stefanie K. , Germain Michael. J.
Published: October 2019

Introduction

Lifestyle interventions have been shown to produce favorable changes in some health outcomes in patients with chronic kidney disease (CKD). However, few such studies, employing “real world” methods have been completed in patients with CKD.

Objective

This study tested the effectiveness of a comprehensive, multicomponent, lifestyle intervention, delivered through individualized counseling on a variety of health outcomes in pre-dialysis CKD patients.

Methods

Eligible patients were assigned randomly to the intervention (TR) or usual care group (UC). A six-month home-based program involving personalized counseling to increase physical activity to recommended levels among stage G3a to G4 CKD patients while exchanging plant proteins for animal proteins was implemented. Physical function, cardiovascular function, dietary intake, medication use, and health-related quality of life (HRQOL) were assessed at baseline and after 1-month, 3-months (M3) and 6-months (M6).

Results

Forty-two, patients (age 60.2 ± 9.2, BMI 34.5 ± 7.8) participated in this study (TR=27 UC=15). The intervention reduced (p<0.05) brachial (bSBP) and central systolic blood pressures (cSBP) at month 3 (M3) but both were attenuated at month 6 (M6). Scores on the effect of kidney disease subscale of the HRQOL measure improved in the intervention group at M3 and M6. There was no change in the other measures of HRQOL or in any physical function scores.

Conclusions

This personalized multi-component lifestyle intervention enabled CKD patients to self-report fewer concerns with how CKD affected their daily lives independent of changes in physical function.
Perinatal exposure to lead results in altered DNA methylation in adult mouse liver and blood: Implications for target versus surrogate tissue use in environmental epigenetics
Authors: Svoboda LK , Neier K , Cavalcante R , Tsai Z , Jones TR , Liu S , Goodrich JM , Lalancette C , Colacino JA , Sartor MA , Dolinoy DC
Published: October 2019

Background

DNA methylation is a critical epigenetic mechanism linking early developmental environment to long-term health. In humans, the extent to which toxicant-induced changes in DNA methylation in surrogate tissues, such as blood, mirror those in the target tissues is unclear. The Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET II) consortium was established by the National Institute of Environmental Health Sciences to address the utility of surrogate tissues as proxies for toxicant-induced epigenetic changes in target tissues.

Objectives

The objective of this study was to investigate the effects of perinatal exposure to a human environmentally relevant level (32 ppm in maternal drinking water) of lead (Pb) on liver and blood DNA methylation in adult male and female mice. We hypothesized that developmental Pb exposure would lead to persistent changes in DNA methylation, and that a subset of differentially methylated loci would overlap between liver and blood.

Methods

Enhanced reduced-representation bisulfite sequencing was used to assess DNA methylation in 5 month old Pb-exposed and control mice. Sex-stratified modeling of differential methylation by Pb exposure was conducted using an established bioinformatics pipeline.

Results

Although Pb exposure ceased at 3 weeks of age, we observed thousands of stably modified, sex-specific differentially methylated regions in the blood and liver of Pb-exposed animals, including 44 genomically imprinted loci. In males, we discovered 5 sites that overlapped between blood and liver, and exhibited changes in DNA methylation in the same direction in both tissues.

Conclusions

These data demonstrate that perinatal exposure to Pb induces sex-specific changes in hepatic DNA methylation in adulthood, some of which are also present in blood. Ongoing studies will provide additional exposure-specific insights, and include other epigenetic marks that will enable further refinement of the design and analysis of human studies where target tissues are inaccessible.
“Abnormal vertebral patterns in genetically heterogeneous deceased fetuses and neonates: evidence of selection against variations”
Authors: Schut Pauline C. , Brosens Erwin , Galis Frietson , Ten Broek Clara M. A. , Baijens Inge M.M. , Dremmen Marjolein H.G. , Tibboel Dick , Schol Martin P. , De Klein Annelies , Eggink Alex J. , Cohen-Overbeek Titia E.
Published: October 2019

Objective

To assess the vertebral pattern in a cohort of deceased fetuses and neonates, and to study the possible impact of DNA Copy Number Variations (CNVs) in coding regions and/or disturbing enhancers on the development of the vertebral pattern.

Method

Radiographs of 445 fetuses and infants, deceased between 2009 and 2015, were assessed. Terminations of pregnancies, stillbirths and neonatal deaths were included. Patients were excluded if the vertebral pattern could not be determined. Copy number profiles of 265 patients were determined using single nucleotide polymorphism array.

Results

274/374 patients (73.3%) had an abnormal vertebral pattern. Cervical ribs were present in 188/374 (50.3%) and were significantly more common in stillbirths (69/128 (53.9%)) and terminations of pregnancies (101/188 (53.7%)), compared to live births (18/58, 31.0%, p = 0.006). None of the rare CNVs were recurrent or overlapped candidate genes for vertebral patterning.

Conclusion

The presence of an abnormal vertebral pattern, particularly in the cervical region, could be a sign of disruption at critical, highly interactive and conserved stages of embryogenesis. The vertebral pattern might provide valuable information regarding fetal and neonatal outcome. CNV analyses did not identify a mutual genetic cause for the occurrence of vertebral patterning abnormalities, indicating genetic heterogeneity.
The genetic origins of Saint Helena’s liberated Africans
Authors: Sandoval-Velasco Marcela , Jagadeesan Anuradha , Ávila-Arcos María C. , Gopalakrishnan Shyam , Ramos-Madrigal Jazmín , Víctor Moreno-Mayar J. , Renaud Gabriel , Cruz-Dávalos Diana I. , Johannesdóttir Erna , Watson Judy , Robson-Brown Kate , Pearson Andrew , Helgason Agnar , Gilbert M. Thomas P. , Schroeder Hannes
Published: October 2019

Between the early 16th and late 19th centuries, an estimated 12 million Africans were transported to the Americas as part of the transatlantic slave trade. Following Britain’s abolition of slave trade in 1807, the Royal Navy patrolled the Atlantic and intercepted slave ships that continued to operate. During this period, the island of St Helena in the middle of the South Atlantic served as a depot for “liberated” Africans. Between 1840 and 1867, approximately 27,000 Africans were disembarked on the island. To investigate their origins, we generated genome-wide ancient DNA data for 20 individuals recovered from St Helena. The genetic data indicate that they came from West Central Africa, possibly the area of present-day Gabon and Angola. The data further suggest that they did not belong to a single population, confirming historical reports of cultural heterogeneity among the island’s African community. Our results shed new light on the origins of enslaved Africans during the final stages of the slave trade and illustrate how genetic data can be used to complement and validate existing historical sources.
Variation in Base Composition Underlies Functional and Evolutionary Divergence in Non-LTR Retrotransposons
Authors: Ruggiero Robert P. , Boissinot Stéphane
Published: October 2019

Background

Non-LTR retrotransposons often exhibit base composition that is markedly different from the nucleotide content of their host’s gene. For instance, the mammalian L1 element is AT-rich with a strong A bias on the positive strand, which results in a reduced transcription. It is plausible that the A-richness of mammalian L1 is a self-regulatory mechanism reflecting a trade-off between transposition efficiency and the deleterious effect of L1 on its host. We examined if the A-richness of L1 is a general feature of non-LTR retrotransposons or if different clades of elements have evolved different nucleotide content. We also investigated if elements belonging to the same clade evolved towards different base composition in different genomes or if elements from the same clades evolved towards similar base composition in the same genome.

Results

We found that non-LTR retrotransposons differ in base composition among clades within the same host but also that elements belonging to the same clade differ in base composition among hosts. We showed that nucleotide content remains constant within the same host over extended period of evolutionary time, despite mutational patterns that should drive nucleotide content away from the observed base composition.

Conclusions

Our results suggest that base composition is evolving under selection and may be reflective of the long-term co-evolution between non-LTR retrotransposons and their host. Finally, the coexistence of elements with drastically different base composition suggests that these elements may be using different strategies to persist and multiply in the genome of their host.
Ectopic Expression of Virus Innexins inHeliothis virescensDisrupts Hemocyte-Mediated Encapsulation and Host Viability
Authors: Zhang Peng , Turnbull Matthew W
Published: October 2019

1.

Polydnaviruses are dsDNA viruses associated with endoparasitoid wasps. Delivery of the virus during parasitization of a caterpillar and subsequent virus gene expression is required for production of an amenable environment for parasitoid offspring development. Consequently, understanding of Polydnavirus gene function provides insight into mechanisms of host susceptibility and parasitoid wasp host range. Polydnavirus genes predominantly are arranged in multimember gene families, one of which is thevinnexins, which are virus homologues of insect gap junction genes, theinnexins. Previous studies ofCampoletis sonorensisIchnovirus Vinnexins using various heterologous systems have suggested the four encoded members may provide different functionality in the infected caterpillar host. Here, we expressed two of the members,vnxGandvnxQ2, using recombinant baculoviruses in susceptible host, the caterpillarHeliothis virescens. Following intrahemocoelic injections, we observed >90% of hemocytes (blood cells) were infected, producing recombinant protein. Larvae infected with avinnexin-recombinant baculovirus exhibited significantly reduced molting rates relative to larvae infected with a control recombinant baculovirus and mock infected larvae. Similarly, larvae infected withvinnexin-recombinant baculoviruses were less likely to molt relative to controls, and showed reduced ability to encapsulate chromatography beads in an immune assay. In most assays, the VnxG protein was associated with more severe pathology than VnxQ2. These results, in light of previous findings, support that Polydnavirus Vinnexin gene family members may provide complementary, rather than redundant, effects. This in turn indicates a need to test gene family member functionality across infected hosts for effects to determine member contribution to host range.

2.

Importance

Polydnaviruses are obligate mutualistic associates of highly speciose wasp taxa that parasitize caterpillars. Expression of Polydnavirus-encoded genes in hosts parasitized by wasps is necessary for successful parasitization, and an unusual genome structure including multiple-membered gene families is hypothesized to contribute to host manipulation. We have tested this hypothesis byin vivoexpression of two members of a family of Polydnavirus homologues of Innexins, or insect gap junction proteins. Previous findings demonstrated that the two Vinnexins induce different physiological alterations in heterologous systems. Here, in host caterpillars, we observed differential alteration by the two proteins of host immune cell (hemocyte) bioelectrical physiology and the immune response of encapsulation. Not only do our data suggest a linkage between cellular bioelectricity and immunity in insects, but they support that gene family expansion has functional consequences to both Polydnavirus and host wasp success.
Organic soil amendment with Spent Mushroom Substrate results in fungal colonisation, alters bacterial-fungal co-occurrence patterns and improves plant productivity
Authors: Paula Fabiana S. , Tatti Enrico , Thorn Camilla , Abram Florence , Wilson Jude , O’Flaherty Vincent
Published: October 2019

In agricultural systems based on organic fertilisers, the activity of prokaryotes and fungi is essential for degradation of complex substrates and release of nutrients for plant uptake. Understanding the dynamics of microbial communities in these systems is, therefore, desirable for designing successful management strategies aiming to optimise nutrient availability and to improve plant productivity. Of particular interest is how the microbial inoculum provided by an organic substrate persists in the soil and interacts with soil and plant microbiomes, as these processes may affect the long-term benefits of organic amendments. We aimed to investigate how these dynamics occurred in soil treated with stabilised spent mushroom substrate (SMS), a soil amendment rich in nutrients and complex organic matter. We carried out a 14 weeks soil trial to assess the plant growth promoting properties of the SMS and to monitor the successional processes of the resulting SMS-soil communities compared to a mineral amended control. Bacterial and fungal communities were analysed by high-throughput sequencing at both DNA and RNA (cDNA) levels. Using a combination of computational tools, including SourceTracker and Network analysis, we assessed the persistence of SMS-derived taxa in soil, and the changes in co-occurrence patterns and microbial community structure over time. Prokaryotic and fungal communities presented remarkably distinct trajectories following SMS treatment. The soil prokaryotic communities displayed higher levels of resilience to the changes introduced by SMS treatment and rapidly tended toward a soil-like profile, with low persistence of SMS-derived prokaryotes. In contrast, the SMS fungal community had greater success in soil colonisation during the time monitored. SMS treatment promoted an increase in the participation of fungi in the highly connected fraction of the active community, including fungal taxa of SMS origin. We observed the presence of highly connected microbial guilds, composed by fungal and bacterial taxa with reported capabilities of complex organic matter degradation. Many of these taxa were also significantly correlated with the organic matter content and plant yield, suggesting that these highly connected taxa may play key roles not only in the community structure, but also in the plant-soil system under organic fertilisation.
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

We 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 Brief

Microfluidic 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.

Highlights

Deterministic 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

Whole-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

Statistical 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

Transcriptome-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

Many 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

Objective

Repeat 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.

Methods

A 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.

Results

In 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.

Conclusion

In 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

Mosquitoes 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

Our 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

Purpose

The 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/approach

An 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.

Findings

Results 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/implications

The 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 implications

Both 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/value

To 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

Purpose

To 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/approach

Cases 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.

Findings

Mitigating 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 implications

The illustration of the CLD helps business managers better understand the interactions among risk variables and explains the systemic reasons for SC vulnerability.

Originality/value

This 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.
Antecedents and consequence associated with esports gameplay
Authors: Jang Wooyoung (William) , Byon Kevin K.
Published: October 2019

Purpose

Grounded in the Unified Theory of Acceptance and Use of Technology 2 (UTAUT2) (Venkatesh et al., 2012), the purpose of this paper is to examine the antecedents and consequence associated with esports gameplay by proposing the Esports Consumption (ESC) model, including six determinants of esports gameplay intention (hedonic motivation, habit, price value, perceived effort expectancy, social influence and flow) and behavioral consequence (media consumption intention of esports events) that were linked to esports gameplay.

Design/methodology/approach

The proposed model was tested using the data (n=348) that were collected from esports consumers at two points in time. Per the technology adoption theories (i.e. TAM, UTAUT2), the authors incorporated a temporal separation when measuring the relationship between playing intention and playing behavior. For the purpose of data analysis, CFA and SEM were used to examine the hypothesized model.

Findings

As a result, four determinants (i.e. hedonic motivation, price value, effort expectancy and flow) were identified as the critical factors influencing esports consumers’ esports gameplay intention. Furthermore, the bootstrap method procedure verified that a sequential relationship among esports gameplay intention, esports gameplay and media consumption of esports events.

Originality/value

Theoretically, it has developed a research model that explains various triggers resulting from esports gameplay intention, which is causally linked to esports gameplay and media consumption behavior. Practically, the primary implication has to do with providing information regarding esports consumers’ playing behavior with esports game publishers, which organize esports events and leagues.
Airbnb in the Byron Shire, Australia – bane or blessing?
Authors: von der Heidt Tania , Muschter Sabine , Caldicott Rod , Che Deborah
Published: October 2019

Purpose

Scholarly research into community members’ views on the positive and negative impacts of Airbnb on the local community is sparse, especially in regional Australia. The purpose of this paper is to explore the views of key informants in the Byron Shire of Australia about the impacts of Airbnb on the local community, as well as possible solutions to the problems.

Design/methodology/approach

A qualitative approach of in-depth interviewing using a semi-structured interview guide was used to capture the views regarding the impacts of Airbnb held by 22 key informants in the Byron Shire community. The interview data were analysed using thematic analysis.

Findings

The 22 interviewees identified five main positive impacts of Airbnb on the Byron Shire community and eight main negative impacts of Airbnb. All participants said they wanted more regulation of Airbnb properties to help address the negative impacts of Airbnb in the community. Eight specific recommendations were offered by the interviewees.

Research limitations/implications

The negative impacts of Airbnb felt by local community are more extensive and deleterious than have been accounted for in the literature. Research into community stakeholder perspectives is important, in order to gain a fuller view of the costs and benefits of sharing economy, especially with regard to short-term letting or holiday letting in tourism centres, as well as potential for more sustainable solutions to the issues.

Practical implications

The findings are being used to inform policy makers’ decisions in managing Airbnb in the Shire.

Social implications

The involvement of key informant community members in this study highlights that there is much common ground between different stakeholders. This type of research may help to provide a sense of enfranchisement and empowerment. This is important in fostering a more balanced public debate, as well as more sustainable approaches to managing the issues.

Originality/value

This paper is the first to explore the views of a range of different key informants in the regional tourist area of Byron Shire in Australia with regard to the positive and negative impacts of Airbnb on the local community, as well as possible solutions to the issues raised by Airbnb.
Doing and being: future graduates, careers and Industry 4.0
Authors: Starr-Glass David
Published: October 2019

Purpose

The purpose of this conceptual study is to reflect on “career” and consider the ways in which its meaning and structure have changed and will continue to change during the era of Industry 4.0. It contends that career advice to students and soon-to-be graduates is an integral part of the educational process and that an understanding of the challenges and opportunities presented by career should be initiated within academia.

Design/methodology/approach

The study is a critical reflection on the literature and the present author’s experience and practice in student career advisement, particularly in the management and business sectors. The methodology used is essentially phenomenological, and the central approach is to make sense of the changing construct of career and the ways in which those changes impact relevant stakeholders. The work is not empirically based and may well have limited generalizability. Nevertheless, it is hoped that it will be of particular interest, value and relevancy to students, graduates and those engaged in career-related issues.

Findings

This study contends that the ongoing evolution of career is best understood as a shift from a progressive sequences of “doing” towards a more expansive and meaningful narrative of “being” and becoming. Recognition of this shift, especially for those studying business-centered subjects, will provide graduates with a better map and direction as they embark on their career trajectories.

Originality/value

Graduation success is critically important for individuals, educational institutions and society at large. A fundamental aspect of perceived success, particularly for business school graduates, is the ability to develop a rewarding career trajectory. This study offers original perspectives on career and presents suggestions that may be of value to those who are about to graduate, to their educational institutions and to those who will deal with them in their work and professional futures.