bluuebunny/crossref_metadata_2025 huggingface dataset:
Two cortical representations of voice control are differentially involved in speech fluency
Authors: Neef Nicole E. , Primaßin Annika , von Gudenberg Alexander Wolff , Dechent Peter , Riedel Heiner Christian , Paulus Walter , Sommer Martin
Published: September 2020

Recent studies have identified two distinct cortical representations of voice control in humans, the ventral and the dorsal laryngeal motor cortex. Strikingly, while persistent developmental stuttering has been linked to a white matter deficit in the ventral laryngeal motor cortex, intensive fluency shaping intervention modulated the functional connectivity of the dorsal laryngeal motor cortical network. Currently, it is unknown whether the underlying structural network organization of these two laryngeal representations is distinct or differently shaped by stuttering intervention. Using probabilistic diffusion tractography in 22 individuals who stutter and participated in a fluency shaping intervention, in 18 individuals who stutter and did not participate in the intervention, and in 28 control participants, we here compare structural networks of the dorsal laryngeal motor cortex and the ventral laryngeal motor cortex and test intervention-related white matter changes. We show (i) that all participants have weaker ventral laryngeal motor cortex connections compared to the dorsal laryngeal motor cortex network, regardless of speech fluency, (ii) connections of the ventral laryngeal motor cortex were stronger in fluent speakers, (iii) the connectivity profile of the ventral laryngeal motor cortex predicted stuttering severity, (iv) but the ventral laryngeal motor cortex network is resistant to a fluency shaping intervention. Our findings substantiate a weaker structural organization of the ventral laryngeal motor cortical network in developmental stuttering and imply that assisted recovery supports neural compensation rather than normalization. Moreover, the resulting dissociation provides evidence for functionally segregated roles of the ventral laryngeal motor cortical and dorsal laryngeal motor cortical networks.
Investigation Gene body methylation is under selection inArabidopsis thaliana
Authors: Muyle Aline , Ross-Ibarra Jeffrey , Seymour Danelle K. , Gaut Brandon S.
Published: September 2020

In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation. It has been controversial whether this phenomenon has any functional role. Here, we took advantage of the availability of 876 leaf methylomes inArabidopsis thalianato characterize the population frequency of methylation at the gene level and estimated the site-frequency spectrum of allelic states (epialleles). Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gene body methylation are under significant selection to remain methylated. Conversely, all genes taken together were inferred to be under selection to be unmethylated. The estimated selection coefficients were small, similar to the magnitude of selection acting on codon usage. We also estimated thatA. thalianais losing gene body methylation three-fold more rapidly than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. Finally, we investigated the potential function of gene body methylation through its link with gene expression level. Across genes with polymorphic methylation states, the expression of gene body methylated alleles was consistently and significantly higher than unmethylated alleles. Although it is difficult to disentangle genetic from epigenetic effects, our work suggests that gbM has a small but measurable effect on fitness, perhaps due to its association to a phenotype like gene expression.
Genetic manipulation of insulin/insulin-like growth factor signaling pathway activity has sex-biased effects onDrosophilabody size
Authors: Millington Jason W. , Brownrigg George P. , Basner-Collins Paige J. , Sun Ziwei , Rideout Elizabeth J.
Published: September 2020

InDrosophila, female body size is approximately 30% larger than male body size due to an increased rate of larval growth. While the mechanisms that control this sex difference in body size remain incompletely understood, recent studies suggest that the insulin/insulin-like growth factor signaling pathway (IIS) plays a role in the sex-specific regulation of growth during development. In larvae, IIS activity differs between the sexes, and there is evidence of sex-specific regulation of IIS ligands. Yet, we lack knowledge of how changes to IIS activity impact growth in each sex, as the majority of studies on IIS and body size use single- or mixed-sex groups of larvae and/or adult flies. The goal of our current study was to clarify the requirement for IIS activity in each sex during the larval growth period. To achieve this goal we used established genetic approaches to enhance, or inhibit, IIS activity, and quantified body size in male and female larvae. Overall, genotypes that inhibited IIS activity caused a female-biased decrease in body size, whereas genotypes that augmented IIS activity caused a male-specific increase in body size. This data extends our current understanding of larval growth by showing that most changes to IIS pathway activity have sex-biased effects on body size, and highlights the importance of analyzing data by sex in larval growth studies.
Airway Basal Cells show a dedifferentiated KRT17highPhenotype and promote Fibrosis in Idiopathic Pulmonary Fibrosis
Authors: Jaeger Benedikt , Schupp Jonas Christian , Plappert Linda , Terwolbeck Oliver , Kayser Gian , Engelhard Peggy , Adams Taylor Sterling , Zweigerdt Robert , Kempf Henning , Lienenklaus Stefan , Garrels Wiebke , Nazarenko Irina , Jonigk Danny , Wygrecka Malgorzata , Klatt Denise , Schambach Axel , Kaminski Naftali , Prasse Antje
Published: September 2020

Idiopathic pulmonary fibrosis (IPF) is a fatal disease with limited treatment options. In this study we focus on the profibrotic properties of airway basal cells (ABC) obtained from patients with IPF (IPF-ABC). Single cell RNA sequencing of bronchial brushes revealed extensive reprogramming of IPF-ABC towards a KRT17highPTENlowdedifferentiated cell type. In the 3D organoid model, compared to ABC obtained from healthy volunteers, IPF-ABC give rise to more bronchospheres,de novobronchial structures resembling lung developmental processes, induce fibroblast proliferation and extracellular matrix deposition in co-culture. Intratracheal application of IPF-ABC into minimally injured lungs of Rag2-/-or NRG mice causes severe fibrosis, remodeling of the alveolar compartment, and formation of honeycomb cyst-like structures. Connectivity MAP analysis of scRNA seq of bronchial brushings suggested that gene expression changes in IPF-ABC can be reversed by SRC inhibition. After demonstrating enhanced SRC expression and activity in these cells, and in IPF lungs, we tested the effects of saracatinib, a potent SRC inhibitor previously studied in humans. We demonstrated that saracatinib modifiedin-vitroandin-vivothe profibrotic changes observed in our 3D culture system and novel mouse xenograft model.
An Inducible Model for Unraveling the Effects of Advanced Glycation End-Product Accumulation in Aging Connective Tissues
Authors: Gouldin Austin G. , Brown M. Ethan , Puetzer Jennifer L.
Published: September 2020

Purpose

In connective tissues there is a clear link between increasing age and degeneration. Advanced glycation end-products (AGEs) are believed to play a central role. AGEs are sugar-induced non-enzymatic crosslinks which accumulate in collagen with age and diabetes, altering tissue mechanics and cellular function. Despite ample correlative evidence linking collagen glycation to tissue degeneration, little is known how AGEs impact cell-matrix interactions, limiting therapeutic options. One reason for this limited understanding is AGEs are typically induced using high concentrations of ribose which decrease cell viability, making it impossible to investigate cell-matrix interactions. The objective of this study was to develop a system to trigger AGE accumulation while maintaining cell viability.

Materials and Methods

Using cell-seeded high density collagen gels, we investigated the effect of two systems for AGE induction, ribose at low concentrations (30, 100, and 200 mM) over 15 days of culture and riboflavin (0.25 mM and 0.75mM) induced with blue light for 40 seconds (riboflavin-465 nm).

Results

We found ribose and riboflavin-465 nm treatment produces fluorescent AGE quantities which match and/or exceed human fluorescent AGE levels for various tissues, ages, and diseases, without affecting cell viability or metabolism. Interestingly, a 40 second treatment of riboflavin-465 nm produced similar levels of fluorescent AGEs as 3 days of 100 mM ribose treatment.

Conclusions

Riboflavin-465 nm is a promising method to trigger AGE crosslinks on demandin vivoorin vitrowithout impacting cell viability and offers potential for unraveling the mechanism of AGEs in age and diabetes related tissue damage.
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
Authors: Yamawaki Tracy M. , Lu Daniel R. , Ellwanger Daniel C. , Bhatt Dev , Manzanillo Paolo , Zhou Hong , Yoon Oh Kyu , Homann Oliver , Wang Songli , Li Chi-Ming
Published: September 2020

Background

Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. However, single-cell methods inherently suffer from limitations in the recovery of complete transcriptomes due to the prevalence of cellular and transcriptional dropout events. This issue is often compounded by limited sample availability and limited prior knowledge of heterogeneity, which can confound data interpretation.

Results

Here, we systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluate methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5’ v1 and 3’ v3 methods. We demonstrate that these methods have fewer drop-out events which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures.

Conclusion

Overall, our characterization of immune cell mixtures provides useful metrics, which can guide selection of a high-throughput single-cell RNA-seq method for profiling more complex immune-cell heterogeneity usually foundin vivo.
High throughput instrument to screen fluorescent proteins under two-photon excitation
Authors: Molina Rosana S. , King Jonathan , Franklin Jacob , Clack Nathan , McRaven Christopher , Goncharov Vasily , Flickinger Daniel , Svoboda Karel , Drobizhev Mikhail , Hughes Thomas E.
Published: September 2020

Two-photon microscopy together with fluorescent proteins and fluorescent protein-based biosensors are commonly used tools in neuroscience. To enhance their experimental scope, it is important to optimize fluorescent proteins for two-photon excitation. Directed evolution of fluorescent proteins under one-photon excitation is common, but many one-photon properties do not correlate with two-photon properties. A simple system for expressing fluorescent protein mutants isE. colicolonies on an agar plate. The small focal volume of two-photon excitation makes creating a high throughput screen in this system a challenge for a conventional point-scanning approach. We present an instrument and accompanying software that solves this challenge by selectively scanning each colony based on a colony map captured under one-photon excitation. This instrument, called the GIZMO, can measure the two-photon excited fluorescence of 10,000E. colicolonies in 7 hours. We show that the GIZMO can be used to evolve a fluorescent protein under two-photon excitation.
Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance
Authors: Pimenta Ricardo José Gonzaga , Aono Alexandre Hild , Villavicencio Burbano Roberto Carlos , Coutinho Alisson Esdras , da Silva Carla Cristina , dos Anjos Ivan Antônio , Perecin Dilermando , de Andrade Landell Marcos Guimarães , Gonçalves Marcos Cesar , Pinto Luciana Rossini , de Souza Anete Pereira
Published: September 2020

A major disease affecting sugarcane, a leading sugar and energy crop, is sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV). Despite damages caused by SCYLV, the genetic basis of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic basis of SCYLV resistance using dominant and codominant markers and genotypes of interest for breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them, demonstrating their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.
PPM1D is a neuroblastoma oncogene and therapeutic target in childhood neural tumors
Authors: Milosevic Jelena , Fransson Susanne , Gulyas Miklos , Gallo-Oller Gabriel , Olsen Thale K , Treis Diana , Wickström Malin , Elfman Lotta HM , Sveinbjornsson Baldur , Hertwig Falk , Bartenhagen Christoph , Reinsbach Susanne , Wilhelm Margareta , Abel Frida , Javanmardi Niloufar , Thankaswamy-Kosalai Subazini , Eissler Nina , Kock Anna , Shi Yao , Tanino Keiji , Hehir-Kwa Jane Y , Mensenkamp Arjen , Tytgat Godelieve AM , Kanduri Chandrasekhar , Holmberg Johan , Gisselsson David , Molenaar Jan J , Jongmans Marjolijn , Fischer Matthias , Kool Marcel , Sakaguchi Kazuyasu , Baryawno Ninib , Martinsson Tommy , Johnsen John Inge , Kogner Per
Published: September 2020

Majority of cancers harbor alterations of the tumor suppressorTP53. However, childhood cancers, including unfavorable neuroblastoma, often lackTP53mutations despite frequent loss of p53 function, suggesting alternative p53 inactivating mechanisms.

Here we show that p53-regulatingPPM1Dat chromosome 17q22.3 is linked to aggressive tumors and poor prognosis in neuroblastoma. We identified that WIP1-phosphatase encoded byPPM1D, is activated by frequent segmental 17q-gain further accumulated during clonal evolution, gene-amplifications, gene-fusions or gain-of-function somatic and germline mutations. Pharmacological and genetic manipulation established WIP1 as a druggable target in neuroblastoma. Genome-scale CRISPR-Cas9 screening demonstratedPPM1Dgenetic dependency inTP53wild-type neuroblastoma cell lines, and shRNAPPM1Dknockdown significantly delayed in vivo tumor formation. Establishing a transgenic mouse model overexpressingPPM1Dshowed that these mice develop cancers phenotypically and genetically similar to tumors arising in mice with dysfunctional p53 when subjected to low-dose irradiation. Tumors include T-cell lymphomas harboringNotch1-mutations,Pten-deletions and p53-accumulation, adenocarcinomas andPHOX2B-expressing neuroblastomas establishingPPM1Das abona fideoncogene in wtTP53 cancer and childhood neuroblastoma. Pharmacological inhibition of WIP1 suppressed the growth of neural tumors in nude mice proposing WIP1 as a therapeutic target in neural childhood tumors.
Genome Methylation Predicts Age and Longevity of Bats
Authors: Wilkinson Gerald S. , Adams Danielle M. , Haghani Amin , Lu Ake T. , Zoller Joseph , Breeze Charles E. , Arnold Bryan D. , Ball Hope C. , Carter Gerald , Cooper Lisa Noelle , Dechmann Dina K.N. , Devanna Paolo , Fasel Nicolas J. , Galazyuk Alexander V. , Günther Linus , Hurme Edward , Jones Gareth , Knörnschild Mirjam , Lattenkamp Ella Z. , Li Caesar Z. , Mayer Frieder , Reinhardt Josephine A. , Medellin Rodrigo A. , Nagy Martina , Pope Brian , Power Megan L. , Ransome Roger D. , Teeling Emma C. , Vernes Sonja C. , Zamora-Mejías Daniel , Zhang Joshua , Horvath Steve
Published: September 2020

Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.
Resolving the spatial and cellular architecture of lung adenocarcinoma by multi-region single-cell sequencing
Authors: Sinjab Ansam , Han Guangchun , Treekitkarnmongkol Warapen , Hara Kieko , Brennan Patrick , Dang Minghao , Hao Dapeng , Wang Ruiping , Dai Enyu , Dejima Hitoshi , Zhang Jiexin , Bogatenkova Elena , Sanchez-Espiridion Beatriz , Chang Kyle , Little Danielle R. , Bazzi Samer , Tran Linh , Krysan Kostyantyn , Behrens Carmen , Duose Dzifa , Parra Edwin R. , Raso Maria Gabriela , Solis Luisa M. , Fukuoka Junya , Zhang Jianjun , Sepesi Boris , Cascone Tina , Byers Lauren , Gibbons Don L. , Chen Jichao , Moghaddam Seyed Javad , Ostrin Edwin J. , Rosen Daniel G. , Heymach John V. , Scheet Paul , Dubinett Steven , Fujimoto Junya , Wistuba Ignacio I. , Stevenson Christopher S. , Spira Avrum E. , Wang Linghua , Kadara Humam
Published: September 2020

Little is known of the geospatial architecture of individual cell populations in lung adenocarcinoma (LUAD) evolution. Here, we perform single-cell RNA sequencing of 186,916 cells from 5 early-stage LUADs and 14 multi-region normal lung tissues of defined spatial proximities from the tumors. We show that cellular lineages, states, and transcriptomic features geospatially evolve across normal regions to LUADs. LUADs also exhibit pronounced intratumor cell heterogeneity within single sites and transcriptional lineage-plasticity programs. T regulatory cell phenotypes are increased in normal tissues with proximity to LUAD, in contrast to diminished signatures and fractions of cytotoxic CD8+ T cells, antigen-presenting macrophages and inflammatory dendritic cells. We further find that the LUAD ligand-receptor interactome harbors increased expression of epithelial CD24 which mediates pro-tumor phenotypes. These data provide a spatial atlas of LUAD evolution, and a resource for identification of targets for its treatment.

Statement of significance

The geospatial ecosystem of the peripheral lung and early-stage LUAD is not known. Our multi-region single-cell sequencing analyses unravel cell populations, states, and phenotypes in the spatial and ecological evolution of LUAD from the lung that comprise high-potential targets for early interception.
Loss of Fgf-responsive Pea3 transcription factors results in ciliopathy-associated phenotypes during early zebrafish development
Authors: McFaul Matt E. , Hart Neta , Draper Bruce W.
Published: September 2020

FGF signaling is used reiteratively during development and elicits several different responses, such as cell proliferation, differentiation, or migration. We parsed the complex FGF intracellular response by creating triple homozygous mutants in the Pea3 subgroup of ETS transcription factors, designated3etvmutants. The Pea3 proteins Etv4 and Etv5 are expressed in areas of FGF activity; however, their role in FGF signal transduction as either positive or negative modulators of FGF activity was unclear. Using3etvmutants, we found these genes act redundantly and have phenotypes consistent with known FGF defects in inner ear, pectoral fin, and posterior mesoderm development. Additionally, we uncovered a novel role for the FGF/Pea3 pathway during body axis straightening.3etvlarvae develop a curly-tail up (CTU) phenotype that we linked to mis-regulation of the polycystin and urotensin pathways, which have opposing actions to ensure a straight body orientation along the dorsal-ventral axis. We find that the Etv4/5 transcription factors act as positive regulators of FGF signaling and propose a model where Etv4/5 are required for cilia function downstream of Fgf8a.

Summary Statement

Pea3 transcription factor triple mutants reveal a role for FGF signaling in balancing polycystin and urotensin signaling to achieve a straight body axis.
Asymmetric Functional Gradients in the Human Subcortex
Authors: Guell Xavier , Schmahmann Jeremy D , Gabrieli John DE , Ghosh Satrajit S , Geddes Maiya R
Published: September 2020

A central principle in our understanding of cerebral cortical organization is that homotopic left and right areas are functionally linked to each other, and also connected with structures that share similar functions within each cerebral cortical hemisphere. Here we refer to this concept as interhemispheric functional symmetry (IHFS). While multiple studies have described the distribution and variations of IHFS in the cerebral cortex, descriptions of IHFS in the subcortex are largely absent in the neuroscientific literature. Further, the proposed anatomical basis of IHFS is centered on callosal and other commissural tracts. These commissural fibers are present in virtually all cerebral cortical areas, but almost absent in the subcortex. There is thus an important knowledge gap in our understanding of subcortical IHFS. What is the distribution and variations of subcortical IHFS, and what are the anatomical correlates and physiological implications of this important property in the subcortex? Using fMRI functional gradient analyses in a large dataset (Human Connectome Project, n=1003), here we explored IHFS in human thalamus, lenticular nucleus, cerebellar cortex, and caudate nucleus. Our detailed descriptions provide an empirical foundation upon which to build hypotheses for the anatomical and physiological basis of subcortical IHFS. Our results indicate that direct or driver cerebral cortical afferent connectivity, as opposed to indirect or modulatory cerebral cortical afferent connectivity, is associated with stronger subcortical IHFS in thalamus and lenticular nucleus. In cerebellar cortex and caudate, where there is no variability in terms of either direct vs. indirect or driver vs. modulatory cerebral cortical afferent connections, connectivity to cerebral cortical areas with stronger cerebral cortical IHFS is associated with stronger IHFS in the subcortex. These two observations support a close relationship between subcortical IHFS and connectivity between subcortex and cortex, and generate new testable hypotheses that advance our understanding of subcortical organization.
Chromatin State Dynamics Confers Specific Therapeutic Strategies in Enhancer Subtypes of Colorectal Cancer
Authors: Orouji Elias , Raman Ayush T. , Singh Anand K. , Sorokin Alexey , Arslan Emre , Ghosh Archit K. , Schulz Jonathan , Terranova Christopher J. , Tang Ming , Maitituoheti Mayinuer , Callahan S. Carson , Tomczak Katarzyna J. , Jiang Zhiqin , Davis Jennifer S. , Ghosh Sukhen , Lee Hey Min , Reyes-Uribe Laura , Chang Kyle , Liu Yushua , Chen Huiqin , Azhdarnia Ali , Morris Jeffrey S. , Vilar Eduardo , Carmon Kendra S. , Kopetz Scott , Rai Kunal
Published: September 2020

The extent and function of chromatin state aberrations during colorectal cancer (CRC) progression is not completely understood. Here, by comprehensive epigenomic characterization of 56 tumors, adenomas, and their matched normal tissues, we define the dynamics of chromatin states during the progression of colorectal cancer. H3K27ac-marked active enhancer state could distinguish between different stages of CRC progression. By epigenomic editing, we present evidence that gains of tumor-specific enhancers for crucial oncogenes, such asASCL2andFZD10, was crucial for excessive proliferation. Consistently, combination of MEK plus bromodomain (BET) inhibition was found to have synergistic effects in CRC patient-derived xenograft (PDX) models. Probing inter-tumor heterogeneity, we identified four distinct enhancer subtypes (EpiC), three of which correlate well with previously defined transcriptomic subtypes (CMSs). Importantly, CMS2 can be divided into two EpiC subgroups with significant survival differences. Leveraging such correlation, we devised a combinatorial therapeutic strategy of enhancer-blocking bromodomain inhibitors with pathway-specific inhibitors (PARPi, EGFRi, and TGFβi) for three EPIC groups. Our data suggest that the dynamics of active enhancer underlies colorectal cancer progression and the patient-specific active enhancer patterns govern their unique gene expression patterns which can be leveraged for precision combination therapy.
Expansion and accelerated evolution of 9-exon odorant receptors inPolistespaper wasps
Authors: Legan Andrew W. , Jernigan Christopher M. , Miller Sara E. , Fuchs Matthieu F. , Sheehan Michael J.
Published: September 2020

Independent origins of sociality in bees and ants are associated with independent expansions of particular odorant receptor (OR) gene subfamilies. In ants, one clade within the OR gene family, the 9-exon subfamily, has dramatically expanded. These receptors detect cuticular hydrocarbons (CHCs), key social signaling molecules in insects. It is unclear to what extent 9-exon OR subfamily expansion is associated with the independent evolution of sociality across Hymenoptera, warranting studies of taxa with independently derived social behavior. Here we describe odorant receptor gene family evolution in the northern paper wasp,Polistes fuscatus, and compare it to four additional paper wasp species spanning ~40 million years of divergence. We find 200 functional OR genes inP. fuscatusmatching predictions from neuroanatomy, and more than half of these are in the 9-exon subfamily. Lineage-specific expansions of 9-exon subfamily ORs are tandemly arrayed inPolistesgenomes and exhibit a breakdown in microsynteny relative to tandem arrays in other OR subfamilies. There is evidence of episodic positive diversifying selection shaping ORs in expanded subfamilies, including 9-exon, E, H, and L, but 9-exon ORs do not stand out as selectively diversified amongPolistesspecies. Accelerated evolution has resulted in lower amino acid similarity and highdN/dS among 9-exon ORs compared to other OR subfamilies. Patterns of OR evolution withinPolistesare consistent with 9-exon OR function in CHC perception by combinatorial coding, with both selection and drift contributing to interspecies differences in copy number and sequence.
CyDAP–A fluorescent probe for cytosolic dopamine detection
Authors: Jeng Jing-Yi , Sun Lee , Wang Jia-Chi , Lin Cheng-Yuan , Hung Chih-Ping , Chu Li-An , Chang Hui-Yun , Chiang Ann-Shyn , Sang Tzu-Kang
Published: September 2020

Dopamine (DA) is an essential neurotransmitter modulating motor and cognitive functions. Several neurological disorders, including Parkinson’s disease (PD) and drug addiction, are the result of DA system dysfunction; however, it remains incomplete understood of why DA neuron is selectively more vulnerable than other neurons. Here we utilize the spectral feature of human MAO B (monoamine oxidase B) to design a genetic-amenable, GFP-based fluorescent probe CyDAP. Upon genetic and pharmacological manipulations to elevate the cytosolic DA levels in cells andDrosophilamodels, CyDAP shows enhanced GFP emission, suggesting this probe is feasible for DA detection. Furthermore, we observe that expressing human α-Synuclein inDrosophilaelicited GFP emission from CyDAP, suggesting a link between cytosolic DA imbalance and regional vulnerability in PD context. Importantly, CyDAP can detect the change of cytosolic DA in liveDrosophilabrains, as demonstrated by time-lapse and the 4D light-sheet confocal recording. CyDAP may serve as a tool for evaluating metabolic deregulation of DA in brain models of PD and other DA system-related psychiatric disorders.
Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction
Authors: Chen Chen , Wu Tianqi , Guo Zhiye , Cheng Jianlin
Published: September 2020

Deep learning has emerged as a revolutionary technology for protein residue-residue contact prediction since the 2012 CASP10 competition. Considerable advancements in the predictive power of the deep learning-based contact predictions have been achieved since then. However, little effort has been put into interpreting the black-box deep learning methods. Algorithms that can interpret the relationship between predicted contact maps and the internal mechanism of the deep learning architectures are needed to explore the essential components of contact inference and improve their explainability. In this study, we present an attention-based convolutional neural network for protein contact prediction, which consists of two attention mechanism-based modules: sequence attention and regional attention. Our benchmark results on the CASP13 free-modeling (FM) targets demonstrate that the two attention modules added on top of existing typical deep learning models exhibit a complementary effect that contributes to predictive improvements. More importantly, the inclusion of the attention mechanism provides interpretable patterns that contain useful insights into the key fold-determining residues in proteins. We expect the attention-based model can provide a reliable and practically interpretable technique that helps break the current bottlenecks in explaining deep neural networks for contact prediction.
GSR: geometrical scan registration algorithm for robust and fast robot pose estimation
Authors: Shamsfakhr Farhad , Sadeghi Bigham Bahram
Published: September 2020

Purpose

In this paper, an attempt has been made to develop an algorithm equipped with geometric pattern registration techniques to perform exact, robust and fast robot localization purely based on laser range data.

Design/methodology/approach

The expected pose of the robot on a pre-calculated map is in the form of simulated sensor readings. To obtain the exact pose of the robot, segmentation of both real laser range and simulated laser range readings is performed. Critical points on two scan sets are extracted from the segmented range data and thereby the pose difference is computed by matching similar parts of the scans and calculating the relative translation.

Findings

In contrast to other self-localization algorithms based on particle filters and scan matching, the proposed method, in common positioning scenarios, provides a linear cost with respect to the number of sensor particles, making it applicable to real-time resource-limited embedded robots. The proposed method is able to obtain a sensibly accurate estimate of the relative pose of the robot even in non-occluded but partially visible segments conditions.

Originality/value

A comparison of state-of-the-art localization techniques has shown that geometrical scan registration algorithm is superior to the other localization methods based on scan matching in accuracy, processing speed and robustness to large positioning errors. Effectiveness of the proposed method has been demonstrated by conducting a series of real-world experiments.
High traditional Asian vegetables(ulam) intake relates to better nutritional status, cognition and mood among aging adults from low-income residential areas
Authors: You Yee Xing , Shahar Suzana , Haron Hasnah , Yahya Hanis Mastura , Che Din Normah
Published: September 2020

Purpose

Aging adults from low-income residential areas were found to have poor nutritional status and mental health based on National Health and Morbidity Survey Malaysia (2015). Good nutrient intake contributes positively in averting these problems. Traditional Asian vegetables (ulam) are rich in polyphenols, antioxidants and fibres which could enhance nutritional status and mood state. This study intended to determine the relationship between habitual ulam intake and nutritional status, mood state and cognition among 252 aging Malaysian adults aged 45–80 years from the low-income residential areas in Klang Valley, Malaysia.

Design/methodology/approach

It was a cross-sectional study that used convenient sampling. Advertisement and invitation letters were sent to three selected community centres in Klang Valley prior to data collection. Informed consent was obtained prior to the collection of socio-demographic data. Anthropometric measurement was performed as per standard protocols. Validated surveys were conducted to obtain information on ulam consumption, mood state and cognitive status using validated food frequency questionnaires, Profile of Mood State and Mini-Mental State Examination questionnaires, respectively.

Findings

The average of ulam intake was 20.5 ± 2.5 g/day (½ serving daily). Habitual ulam intake was associated with lower waist circumference (R2 = 0.166, β = −0.216, p < 0.01), better MMSE scores (R2 = 0.337, β = 0.128, p < 0.05), less anger (R2 = 0.081, β = −0.116, p < 0.05), less tension (R2 = 0.139, β = −0.204, p < 0.01) and positive total mood disturbance (R2 = 0.095, β = 0.164, p < 0.05) after adjustment for gender, age, energy intake, total fruits and vegetables (non-ulam) consumption. The ulam intake at 100th percentile (=30g/day) associated to a better nutritional status, mood state and cognitive status in comparison to 25th percentile (<7.9 g/day) (p < 0.05).

Originality/value

Findings from this research would recommend people to consume not less than 1 serving of ulam everyday in order to have improved nutritional status, mood and cognition; nonetheless, future studies are required to clarify the causal mechanism concerning this relationship.
Interdiscursivity in corporate financial communication: an analysis of earnings videos
Authors: Rajandran Kumaran
Published: September 2020

Purpose

Financial communication produces various texts, among which are earnings videos. The videos employ language and image in multimodal discourses to convey specific social meanings about corporate performance. The purpose of this paper is to select earnings videos and study their incorporated genres, styles and discourses.

Design/methodology/approach

Interdiscursivity permits hybridity because it mixes the choice of genres, styles or discourses. An interdiscursive analysis is conducted on earnings videos in English, French and Spanish from corporations in the global finance industry. It involved three sequential stages: (1) to detect the discourses, (2) to name the discourses and (3) to consider the function of the discourses.

Findings

Earnings videos are hybrid because interview and presentation genres, formal and casual styles and the discourses of financial accounting, strategic management and public relations are encountered. The genres, styles and discourses are interwoven to create an interdiscursive mix, which constructs earnings through a (pseudo)personal social relation and easified discourses. The multimodal discourses convey robust corporate performance in an interim, and their use is symptomatic of marketization. Corporations may “market” their performance to seem like a worthwhile investment to persuade (potential) investors.

Originality/value

The paper enriches existing research in financial communication because it studies how multimodal discourses in earnings videos are tailored for marketization. The videos have not been analyzed, and their analysis complements earlier studies on other financial communication texts. The analysis examines discourses through language and image features, whose co-deployment conveys meaning about corporations.
Political sensitivity and government oversight in the US corporate bond market: evidence from federal contractors
Authors: Craig Karen Ann , Hadley Brandy
Published: September 2020

Purpose

This paper aims to investigate the political cost hypothesis and the effects of political sensitivity-induced governance in the US bond market by using yield spreads from bonds issued by a diverse sample of US government contractors.

Design/methodology/approach

Fixed effects regression analysis is used to test the relation between the political sensitivity of government contractor firms and their cost of debt.

Findings

Results illustrated that government contractors with greater political sensitivity are associated with larger yield spreads, indicating that bondholders require a premium when firms endure the costs of increased political oversight and the threat of outside intervention, reducing the certainty of future income. However, despite the overall positive impact of political sensitivity on bond yield spreads on average, the authors found that the additional government oversight is associated with lower spreads when the firm is facing greater repayment risk.

Practical implications

Despite the benefits of winning a government contract, this paper identifies a direct financial cost of increased political sensitivity because of additional firm oversight and potential intervention. Importantly, it also finds that this governance is valued by bondholders when faced with increased risk. Firms must balance their desire for government receipts with the costs and benefits of dependence on those expenditures.

Originality/value

This paper contributes to the literature in its exploration of political sensitivity as an important determinant of the cost of debt for corporate government contractors. Specifically, the authors document a significant risk premium in bond pricing because of the joint effects of the visibility and importance of government contracts to the firm.
Exploring consumer–brand engagement: a holistic framework
Authors: Cheung Man Lai , Pires Guilherme D. , Rosenberger III Philip J.
Published: September 2020

Purpose

This paper aims to investigate the causal relationships between constructs related to consumer–brand engagement (CBE), including consumers’ enduring involvement, ongoing information search behaviour, online engagement behaviour and brand attitude in Hong Kong.

Design/methodology/approach

The theoretical framework is tested using data from 302 customers of a durable technology product, a smartphone, in Hong Kong, collected using a self-administered online survey. Partial least squares-structural equation modelling was used to analyse the data.

Findings

The results reveal that consumers’ enduring involvement and ongoing information search behaviour are key drivers of CBE, ultimately enhancing customers’ brand attitude. The importance of enduring involvement in strengthening ongoing search behaviour, online engagement behaviour and CBE is confirmed, together with the importance of ongoing search behaviour in strengthening CBE. Further analysis demonstrated the full mediating role of ongoing search behaviour in the relationship between enduring involvement and online engagement behaviour, such that CBE fully mediates the impact of ongoing search behaviour on brand attitude.

Research limitations/implications

The research contributes to the extant literature by providing an understanding of how to strengthen CBE for durable technology products, such as smartphones. However, this study is cross-sectional in nature, focusing on smartphones in Hong Kong only. Thus, future research should consider comparisons between countries with diverse cultures as well as other industries, such as the service sector, to enhance the generalisability of the study’s findings.

Practical implications

Marketers should seek to heighten customers’ involvement levels by encouraging customer–brand interactions, which is not only useful in encouraging customers’ ongoing search and online engagement behaviour but also critical in strengthening CBE. Additionally, marketers are recommended to encourage customers’ ongoing search behaviour (at the category level), which is useful in encouraging consumers’ online engagement behaviour as well as strengthening CBE.

Originality/value

The role of ongoing search behaviour in brand building has received little attention in the branding literature. This paper makes a noteworthy contribution to CBE research by empirically testing a holistic framework, confirming that enduring involvement and ongoing search behaviour are critical drivers in the process of strengthening CBE. This paper also demonstrates the mediation roles of ongoing search behaviour and CBE in the holistic framework.
Manufacturing intelligent Corvus corone module for a secured two way image transmission under WSN
Authors: Alhayani Bilal , Abdallah Abdallah Ali
Published: September 2020

Purpose

The manufacturing of intelligent and secure visual data transmission over the wireless sensor network is key requirement nowadays to many applications. The two-way transmission of image under a wireless channel needed image must compatible along channel characteristics such as band width, energy-efficient, time consumption and security because the image adopts big space under the device of storage and need a long time that easily undergoes cipher attacks. Moreover, Quizzical the problem for the additional time under compression results that, the secondary process of the compression followed through the acquisition consumes more time.

Design/methodology/approach

Hence, for resolving these issues, compressive sensing (CS) has emerged, which compressed the image at the time of sensing emerges as a speedy manner that reduces the time consumption and saves bandwidth utilization but fails under secured transmission. Several kinds of research paved path to resolve the security problems under CS through providing security such as the secondary process.

Findings

Thus, concerning the above issues, this paper proposed the Corvus corone module two-way image transmission that provides energy efficiency along CS model, secured transmission through a matrix of security under CS such as inbuilt method, which was named as compressed secured matrix and faultless reconstruction along that of eminent random matrix counting under CS.

Originality/value

Experimental outputs shows intelligent module gives energy efficient, secured transmission along lower computational timing also decreased bit error rate.
An h-version adaptive FEM for eigenproblems in system of second order ODEs: vector Sturm-Liouville problems and free vibration of curved beams
Authors: Wang Yongliang
Published: September 2020

Purpose

This study aims to overcome the involved challenging issues and provide high-precision eigensolutions. General eigenproblems in the system of ordinary differential equations (ODEs) serve as mathematical models for vector Sturm-Liouville (SL) and free vibration problems. High-precision eigenvalue and eigenfunction solutions are crucial bases for the reliable dynamic analysis of structures. However, solutions that meet the error tolerances specified are difficult to obtain for issues such as coefficients of variable matrices, coincident and adjacent approximate eigenvalues, continuous orders of eigenpairs and varying boundary conditions.

Design/methodology/approach

This study presents an h-version adaptive finite element method based on the superconvergent patch recovery displacement method for eigenproblems in system of second-order ODEs. The high-order shape function interpolation technique is further introduced to acquire superconvergent solution of eigenfunction, and superconvergent solution of eigenvalue is obtained by computing the Rayleigh quotient. Superconvergent solution of eigenfunction is used to estimate the error of finite element solution in the energy norm. The mesh is then, subdivided to generate an improved mesh, based on the error.

Findings

Representative eigenproblems examples, containing typical vector SL and free vibration of beams problems involved the aforementioned challenging issues, are selected to evaluate the accuracy and reliability of the proposed method. Non-uniform refined meshes are established to suit eigenfunctions change, and numerical solutions satisfy the pre-specified error tolerance.

Originality/value

The proposed combination of methodologies described in the paper, leads to a powerful h-version mesh refinement algorithm for eigenproblems in system of second-order ODEs, that can be extended to other classes of applications in damage detection of multiple cracks in structures based on the high-precision eigensolutions.
Tuning into rebellious matter: affective literacies as more-than-human sonic bodies
Authors: Dernikos Bessie Patricia
Published: September 2020

Purpose

The purpose of this paper is to explore the sonic vibrations, infectious rhythms and alternative frequencies that are often unheard and overlooked within mainstream educational spaces, that is, perceptually coded out of legibility by those who read/see/hear the world through “whiteness.”

Design/methodology/approach

“Plugging into” (Jackson and Mazzei, 2012) posthuman theories of affect (Deleuze and Guattari, 1987; Henriques, 2010) and assemblage (Weheliye, 2014), the author argues that “literate bodies,” along with all forms of matter, continually vibrate, move, swell and rebel (Deleuze, 1990), creating momentum that is often difficult not to get tangled up in.

Findings

This paper maps out how a specific sociohistorical concept of sound works to affectively orient bodies and impact student becomings, namely, by producing students as un/successful readers and in/human subjects. At the same time, the author attends to the subtle ways by which first graders rebelliously move (d) with alternative sonic frequencies to resist/disrupt mandated literacy curricula and white, patriarchal ways of knowing, being and doing.

Originality/value

This paper highlights the political nature of sound and how, within mainstream educational spaces, certain sonic frequencies become coded out of white supremacist models for knowledge transmission, which re/produce racialized (gendered, classist, etc.) habits and practices of listening/hearing. Literacy educators are invited to “(re)hear” the social in more just ways (James, 2020) by sensing the affects and effects of more-than-human “sonic bodies” (Henriques, 2011), which redirect us to alternative rhythms, rationalities, habits and practices that challenge normative conceptions of what counts as literacy and who counts as successfully literate.