bluuebunny/crossref_metadata_2025 huggingface dataset:
A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress
Authors: Stephani Madlen , Picchianti Lorenzo , Gajic Alexander , Beveridge Rebecca , Skarwan Emilio , de Medina Hernandez Victor Sanchez , Mohseni Azadeh , Clavel Marion , Zeng Yonglung , Naumann Christin , Matuszkiewicz Mateusz , Turco Eleonora , Loefke Christian , Li Baiying , Durnberger Gerhard , Schutzbier Michael , Chen Hsiao Tieh , Abdrakhmanov Alibek , Savova Adriana , Chia Khong-Sam , Djamei Armin , Schaffner Irene , Abel Steffen , Jiang Liwen , Mechtler Karl , Ikeda Fumiyo , Martens Sascha , Clausen Tim , Dagdas Yasin
Published: March 2020

Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the ER. Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism. However, the degree to which ER-phagy is employed by other branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that bridges selective autophagy with ribosome-associated quality control at the ER.
Integrated lipidomics and proteomics network analysis highlights lipid and immunity pathways associated with Alzheimer’s disease
Authors: Xu Jin , Bankov Giulia , Kim Min , Wretlind Asger , Lord Jodie , Green Rebecca , Hodges Angela , Hye Abdul , Aarsland Dag , Velayudhan Latha , Dobson Richard J.B. , Proitsi Petroula , Legido-Quigley Cristina ,   on behalf of the AddNeuroMed Consortium
Published: March 2020

INTRODUCTION

There is an urgent need to understand the molecular mechanisms underlying Alzheimer’s Disease (AD) to enable early diagnosis and develop effective treatments. Here we aim to investigate Alzheimer’s dementia using an unsupervised lipid, protein and gene multi-omic integrative approach.

METHODS

A lipidomics dataset (185 AD, 40 MCI and 185 controls) and a proteomics dataset (201 AD patients, 104 MCI individuals and 97 controls) were utilised for weighted gene co-expression network analyses (WGCNA). An additional proteomics dataset (94 AD, 55 MCI and 100 controls) was included for external proteomics validation. Modules created within each modality were correlated with clinical AD diagnosis, brain atrophy measures and disease progression, as well as with each other. Gene Ontology (GO) enrichment analysis was employed to examine the biological processes and molecular and cellular functions for protein modules associated with AD phenotypes. Lipid species were annotated in the lipid modules associated with AD phenotypes. Associations between established AD risk loci and lipid/protein modules that showed high correlation with AD phenotypes were also explored.

RESULTS

Five of the 20 identified lipid modules and five of the 17 identified protein modules were correlated with AD phenotypes. Lipid modules comprising of phospholipids, triglycerides, sphingolipids and cholesterol esters, correlated with AD risk loci involved in immune response and lipid metabolism. Five protein modules involved in positive regulation of cytokine production, neutrophil mediated immunity, humoral immune responses were correlated with AD risk loci involved in immune and complement systems.

DISCUSSION

We have shown the first multi-omic study linking genes, proteins and lipids to study pathway dysregulation in AD. Results identified modules of tightly regulated lipids and proteins that were strongly associated with AD phenotypes and could be pathology drivers in lipid homeostasis and innate immunity.

Research in Context

Lipid and protein modules were preserved amongst Alzheimer’s disease (AD) patients, participants with mild cognitive impairment (MCI) and controls. Protein modules were also externally validated.

Five lipid and five protein modules out of a total of thirty-seven correlated with clinical AD diagnosis, brain atrophy measurements and the rate of cognitive decline in AD.

Lipid and protein modules associated with AD phenotypes showed associations with established AD risk loci involved in lipid and immune pathways.
A Data-Independent-Acquisition-based proteomic approach towards understanding the acclimation strategy ofMicrochloropsis gaditanaCCMP526 in hypersaline conditions
Authors: Karthikaichamy Anbarasu , Beardall John , Coppel Ross , Noronha Santosh , Bulach Dieter , Schittenhelm Ralf B , Srivastava Sanjeeva
Published: March 2020

Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants.Microchloropsis gaditanaCCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipids as an energy storage molecule. We used proteomics to understand the molecular basis for acclimation ofM. gaditanato increased salinity levels (55 and 100 PSU (Practical Salinity Unit). Correspondence analysis (CA) was used for the identification of salinity-responsive proteins (SRPs). The highest number of altered proteins was observed in 100 PSU. Gene Ontology (GO) enrichment analysis revealed a separate path of acclimation for cells exposed to 55 and 100 PSU. Osmolyte and lipid biosynthesis was up-regulated in high saline conditions. However, concomitantly lipid oxidation pathways were also up-regulated at high saline conditions, providing acetyl-CoA for energy metabolism through the TCA cycle. Carbon fixation and photosynthesis were tightly regulated, while chlorophyll biosynthesis was affected under high salinity conditions. Importantly, temporal proteome analysis of salinity-challengedM. gaditanarevealed vital salinity-responsive proteins which could be used for strain engineering for improved salinity resistance.
Cooperative Chikungunya virus membrane fusion and its sub-stoichiometric inhibition by CHK-152 antibody
Authors: Blijleven Jelle S. , Bouma Ellen M. , van Duijl Mareike K.S. , Smit Jolanda M. , van Oijen Antoine M.
Published: March 2020

Chikungunya virus (CHIKV) presents a major burden on healthcare systems worldwide, but specific treatment remains unavailable. Attachment and fusion of CHIKV to the host cell membrane is mediated by the E1/E2 protein spikes. We used an in vitro single-particle fusion assay to study the effect of the potent, neutralizing antibody CHK-152 on CHIKV binding and fusion. We find that CHK-152 shields the virions, inhibiting interaction with the target membrane and inhibiting fusion. Analysis of the ratio of bound antibodies to epitopes implied that CHIKV fusion is a highly cooperative process. Further, dissociation of the antibody at lower pH results in a finely balanced kinetic competition between inhibition and fusion, suggesting a window of opportunity for the spike proteins to act and mediate fusion even in the presence of antibody.
A Novel Machine Learning Approach Uncovers New and Distinctive Inhibitors for Cyclin-Dependent Kinase 9
Authors: Assmann Mariana , Bal Matthias , Craig Michael , D’Oyley Jarryl , Phillips Lawrence , Triendl Hagen , Bates Paul A. , Bashir Usman , Ruprah Parminder , Shaker Noor , Stojevic Vid
Published: March 2020

We present a novel combination of generative and predictive machine learning models for discovering unique protein inhibitors. The new method is assessed on its ability to generate unique inhibitors for the cancer associated protein kinase, CDK9. We validate our method by performing biochemical assays, attaining a hit rate of more than 10%, demonstrating the method to be a notable improvement upon a more standard, and somewhat naive approach. Moreover, we imposed the additional challenge of finding inhibitors that are readily synthesized. Importantly, two new inhibitors are found, with one being distinct from reported CDK9 inhibitors. We discuss the results in the context of modern machine learning principles and the desire expressed by the rational drug design community to secure molecules that are structurally different, yet with high binding affinities, to structurally determined protein targets.
A Combinatorial Approach of Biparental QTL Mapping and Genome-Wide Association Analysis Identifies Candidate Genes for Phytophthora Blight Resistance in Sesame
Authors: Sovetgul Asekova , Oh Eunyoung , Kulkarni Krishnanand P. , Lee Myoung Hee , In Kim Jung , Pae Suk-Bok , Kim Minsu , Oh Ki-Won , Cho Kwang-Soo , Kim Sungup
Published: March 2020

Phytophthora blight, caused by pathogenPhytophthora nicotianae, is responsible for a huge reduction in sesame (Sesamum indicumL.) crop yields. In this study, we utilized a combinatorial approach involving biparental QTL mapping and genome-wide association (GWAS) analysis to identify genes associated with Phytophthora blight resistance in sesame. Evaluation of resistant of the parental varieties (Goenbaek, Osan and Milsung) and the RILs of both the populations in greenhouse conditions suggested the qualitative nature of the trait.. The genetic map comprised thirteen LGs covering a total map length of 887.49 cM with an average inter-marker distance of 4.69 cM. Significant QTLs explaining phenotypic variation in the range of 2.25% to 69.24% were identified on chromosomes 10 and 13 (Chr10 and Chr13). A resistance locus detected on Chr10 was found to be highly significant. The association of this locus to PBR was also identified through BSA and single marker analysis in Goenbaek × Milsung cross and through genome-wide association mapping of 87 sesame accessions. The GWAS analysis identified 44 SNP loci significantly associated with Phytophthora disease-resistant traits on Chr10. Further, the haplotype block analysis conducted in order to find whether the SNPs associated with resistance in this study showed that the SNPs are in high LD with the resistance QTL. We obtained a total of 68 candidate genes, which included a number of defense-relatedRgenes. One of the genes,SIN_1019016(At1g58390)showed high expression in the resistant parent. The results from this study would be highly useful in identifying genetic and molecular factors associated with Phytophthora blight resistance in sesame.
Variability within rare cell states enables multiple paths towards drug resistance
Authors: Emert Benjamin L. , Cote Christopher , Torre Eduardo A. , Dardani Ian P. , Jiang Connie L. , Jain Naveen , Shaffer Sydney M. , Raj Arjun
Published: March 2020

Molecular differences between individual cells can lead to dramatic differences in cell fate, such as death versus survival of cancer cells upon drug treatment. These originating differences remain largely hidden due to difficulties in determining precisely what variable molecular features lead to which cellular fates. Thus, we developed Rewind, a methodology that combines genetic barcoding with RNA FISH to directly capture rare cells that give rise to cellular behaviors of interest. Applied to BRAFV600Emelanoma, we trace drug-resistant cell fates back to single-cell gene expression differences in their drug-naive precursors (initial frequency of ∼1:1000-1:10,000 cells) and relative persistence of MAP-kinase signaling soon after drug treatment. Within this rare subpopulation, we uncover a rich substructure in which molecular differences between several distinct subpopulations predict future differences in phenotypic behavior, such as proliferative capacity of distinct resistant clones following drug treatment. Similarly, we show that treatments that modify the frequency of resistance can allow otherwise non-resistant cells in the drug-naive population to become resistant, and that these new populations are marked by the variable expression of distinct genes. Together, our results reveal the presence of hidden, rare-cell variability that can underlie a range of latent phenotypic outcomes upon drug exposure.
Trpm8modulates thermogenesis in a sex-dependent manner without influencing cold-induced bone loss
Authors: Carvalho Adriana Lelis , Treyball Annika , Brooks Daniel J. , Costa Samantha , Neilson Ryan J. , Reagan Michaela R. , Bouxsein Mary L. , Motyl Katherine J.
Published: March 2020

Trpm8(transient receptor potential cation channel, subfamily M, member 8) is expressed by sensory neurons, and it is involved in the detection of cold temperatures. Increased TRPM8 activity triggers an increase in uncoupling protein 1 (Ucp1)-dependent brown adipose tissue (BAT) thermogenesis. Bone density and marrow adipose tissue are regulated by rodent housing temperature and brown adipose tissue, suggesting one mediator of this effect may be TRPM8. In order to test whether TRPM8 was involved in the co-regulation of thermogenesis and bone homeostasis, we examined the bone phenotypes of one-year-oldTrpm8knockout mice (Trpm8-KO) and then exposed them to a 4-week cold temperature challenge. MaleTrpm8-KOmice had lower bone mineral density than WT, with smaller bone size (femur length and cross-sectional area) being the most striking finding, and exhibited a delayed cold acclimation with increased BAT expression ofUcp1, Dio2andCideaat the end of the study. In contrast to males, femaleTrpm8-KOmice had low vertebral bone microarchitectural parameters, but no genotype-specific alterations in body temperature. Interestingly,Trpm8was not required for cold-induced trabecular bone loss in either sex, but may be required for cold-induced changes in marrow adiposity in males. Furthermore, bone marrow adipose tissue accumulation in females was significantly blunted byTrpm8deletion. In summary, we identified sex differences in the role of TRPM8 in maintaining body temperature, bone density and marrow adipose tissue. Identifying mechanisms through which cold temperature and brown adipose tissue influence bone could help to ameliorate potential bone side effects of obesity treatments designed to stimulate thermogenesis.
APOL1 variant-expressing endothelial cells exhibit autophagic dysfunction and mitochondrial stress
Authors: Blazer Ashira , Qian Yingzhi , Schlegel Martin Paul , Buyon Jill P. , Cadwell Ken , Cammer Michael , Heffron Sean P. , Liang Feng-Xia , Mehta-Lee Shilpi , Niewold Timothy , Rasmussen Sara E. , Clancy Robert M.
Published: March 2020

Apolipoprotein L1 (APOL1) gene risk variants (RV) associate with renal and cardiovascular disease particularly in SLE. We hypothesized that in RV-carrying human umbilical vein endothelial cells (HUVECs) cytokine-induced APOL1 expression compromises mitochondrial respiration, lysosome integrity, and autophagic flux. HUVEC cultures of each APOL1 genotype were generated. APOL1 was expressed using IFNɣ; HUVEC mitochondrial function, lysosome integrity, and autophagic flux were measured. IFNɣ increased APOL1 expression across all genotypes 20-fold (p=0.001). Compared to the homozygous G0 (ancestral) allele (0RV), high risk (2RV) HUVECs showed both depressed baseline and maximum mitochondrial oxygen consumption (p<0.01), and impaired mitochondrial networking on MitoTracker assays. These cells also demonstrated a contracted lysosome compartment (p<0.001), and an accumulation of autophagosomes suggesting a defect in autophagic flux. Treatment of 0RV HUVECs with a non-selective lysosome inhibitor, hydroxychloroquine, produced autophagosome accumulations similar to the 2RV cells, thus implicating lysosome dysfunction in blocking autophagy. Compared to 0RV and 2RV HUVECs, 1 RV cells demonstrated an intermediate autophagy defect which was exacerbated by IFNɣ. Our findings implicate dysfunction of mitochondrial respiration, lysosome, and autophagy in APOL1 RV-mediated endothelial cytotoxicity. IFNɣ amplified this phenotype even in variant heterozygous cells–a potential underpin of the APOL1/inflammation interaction. This is the first description of APOL1 pathobiology in variant heterozygous cell cultures.
Orchard layout and plant traits influence fruit yield more strongly than pollinator behaviour and density in a dioecious crop
Authors: Peace Angela , Pattermore David , Broussard Melissa , Fonseka Dilini , Tomer Nathan , Bosque-Pérez Nilsa A. , Crowder David , Shaw Allison K. , Jesson Linley , Howlett Brad , Jochym Mateusz , Li Jing
Published: March 2020

Mutualistic plant-pollinator interactions are critical for the functioning of both non-managed and agricultural systems. Mathematical models of plant-pollinator interactions can help understand key determinants in pollination success. However, most previous models have not addressed pollinator behavior and plant biology combined. Information generated from such a model can inform optimal design of crop orchards and effective utilization of managed pollinators like honey bees, and help generate hypotheses about the effects of management practices and cultivar selection. We expect that honey bee density per flower and male to female flower ratio will influence fruit yield. To test the relative importance of these effects, both singly and simultaneously, we utilized a delay differential equation model combined with Latin hypercube sampling for sensitivity analysis. Empirical data obtained from historical records and collected in kiwifruit orchards in New Zealand were used to parameterize the model. We found that, at realistic bee densities, the optimal orchard had 65-75% female flowers, and the most benefit was gained from the first 6-8 bees/1000 flowers, with diminishing returns thereafter. While bee density significantly impacted fruit production, plant-based parameters-flower density and male:female flower ratio-were the most influential. The predictive model provides strategies for improving crop management.
Erosion of human X chromosome inactivation causes major remodelling of the iPSC proteome
Authors: Brenes Alejandro J. , Yoshikawa Harunori , Bensaddek Dalila , Mirauta Bogdan , Seaton Daniel , Hukelmann Jens L. , Jiang Hao , Stegle Oliver , Lamond Angus I.
Published: March 2020

X chromosome inactivation (XCI) is a dosage compensation mechanism in female mammals whereby genes from one X chromosome are repressed. Analysis of human induced pluripotent stem cell (iPSC) lines using proteomics, RNAseq and polysome profiling showed a major change in the proteome upon XCI erosion. This resulted in amplified RNA and protein expression from X-linked genes. However, increased protein expression was also detected from autosomal genes without a corresponding mRNA increase, altering the protein-RNA correlation between genes on the X chromosome and autosomes. Eroded iPSC lines display ~13% increase in cell protein content, along with increased expression of ribosomal proteins, ribosome biogenesis and translation factors. They also showed significantly increased levels of active polysomes within the eroded lines. We conclude that erosion of XCI causes a major remodelling of the proteome, with translational mechanisms affecting the expression of a much wider range of proteins and disease-linked loci than previously realised.
Accurate 4Pi single-molecule localization using an experimental PSF model
Authors: Li Yiming , Buglakova Elena , Zhang Yongdeng , Thevathasan Jervis Vermal , Bewersdorf Joerg , Ries Jonas
Published: March 2020

Interferometric single-molecule localization microscopy (iPALM, 4Pi-SMS) uses multiphase interferometry to localize single fluorophores and achieves nanometer isotropic resolution in 3D. The current data analysis workflow, however, fails to reach the theoretical resolution limit due to the suboptimal localization algorithm. Here, we develop a method to fit an experimentally derived point spread function (PSF) model to the interference 4Pi-PSF. As the interference phase is not fixed with respect to the shape of the PSF, we decoupled the phase term in the model from the 3D position of the PSF. The fitter can reliably infer the interference period even without introducing astigmatism, reducing the complexity of the microscope. Using a spline-interpolated experimental PSF model and by fitting all phase images globally, we show on simulated data that we can achieve the theoretical limit of 3D resolution, the Cramer-Rao lower bound (CRLB), also for the 4Pi microscope.
Lipid metabolic stress in development defines which genetically-susceptible DYT-TOR1Amice develop disease
Authors: Cascalho Ana , Foroozandeh Joyce , Rous Stef , Martínez Vizcaíno Natalia , Gallego Sandra F. , Goodchild Rose E.
Published: March 2020

There has been enormous progress defining the genetic landscape of disease. However, genotypes rarely fully predict neurological phenotypes, and we rarely understand why.TOR1A+/Δgag that causes dystonia with ~30% penetrance is a classic case. Here we show, in inbred mice, that +/Δgag affects embryonic brain lipid metabolism with sex-skewed reduced penetrance. Penetrance is affected by environmental context, including maternal diet. The lipid metabolic defect resolves during post-natal development. Nevertheless, we discover dystonia-like symptoms in ~30% of juvenile femaleTor1a+/Δgagmice, and prevent these symptoms by genetically suppressing abnormal lipid metabolism. We conclude thatTor1a+/Δgagembryos poorly buffer metabolic stressin utero, resulting in a period of abnormal metabolism that hardwires the brain for dystonia in later life. The data show unexpected and profound impacts of sex, and thus highlight the importance of examining male and female animal models of disease.

Significance Statement

The genetic landscape of neurological disease is relatively well mapped. However, we typically cannot explain why some mutations only cause disease in a subset of individuals. A classic case is DYT-TOR1Adystonia that only develops in 30% ofTOR1A+/Δgagcarriers. We now find that ~30% of inbred femaleTor1a+/Δgagmice develop abnormal brain lipid metabolism as embryos, while males are spared. The percentage is affected by maternal diet. Further, this period of abnormal lipid metabolism causes dystonia-like symptoms in juvenile mice. These data show how an environmentally-sensitive event of development defines which genetically-susceptible individuals develop disease in later life. They also highlight the importance of examining male and female animal models of disease.
EMU: reconfigurable graphical user interfaces for Micro-Manager
Authors: Deschamps Joran , Ries Jonas
Published: March 2020

Advanced light microscopy methods are becoming increasingly popular in biological research. Their ease of use depends, besides experimental aspects, on intuitive user interfaces. The open-source software Micro-Manager offers a universal interface for microscope control but requires implementing plugins to further tailor it to specific systems. Since even similar devices can have different Micro-Manager properties (such as power percentage versus absolute power), transferring user interfaces to other systems is usually very restricted.

We developed Easier Micro-Manager User interface (EMU), a Micro-Manager plugin, to simplify building flexible and reconfigurable user interfaces. EMU offers a choice of interfaces that are rapidly ready to use thanks to an intuitive configuration menu. In particular, the configuration menu allows mapping device properties to the various functions of the interface in a few clicks. Exchanging or adding new devices to the microscope no longer requires rewriting code. The EMU framework also simplifies implementing a new interface by providing the configuration and device interaction mechanisms. The user interface can be built by using a drag-and-drop tool in one’s favorite Java development environment and writing a few lines of code for compatibility with EMU.

Micro-Manager users now have a powerful tool to improve the user experience on their instruments. EMU interfaces can be easily transferred to new microscopes and shared with other research groups. In the future, newly developed interfaces will be added to EMU to benefit the whole community.
Auxin Regulation andMdPINExpression during Adventitious Root Initiation in Apple Cuttings
Authors: Guan Ling , Li Yingjun , Huang Kaihui , Cheng Zong-Ming (Max)
Published: March 2020

Adventitious root (AR) formation is critical for the efficient propagation of elite horticultural and forestry crops. Despite decades of research, the cellular processes and molecular mechanisms underlying AR induction in woody plants remains obscure. We examined the details of AR formation in the apple (Malus domestica) M.9 rootstock, the most widely used dwarf rootstock for intensive production, and investigated the role of polar auxin transport in post-embryonic organogenesis. AR formation begins with a series of founder cell divisions and elongation of interfascicular cambium adjacent to vascular tissues. This process was associated with a relatively high indole acetic acid (IAA) content and hydrolysis of starch grains. Exogenous auxin treatment promoted cell division, as well as the proliferation and reorganization of the endoplasmic reticulum and Golgi membrane. By contrast, treatment with the auxin transport inhibitorN-1-naphthylphthalamic acid (NPA) inhibited cell division in the basal region of the cutting and resulted in abnormal cell divisions during early AR formation. In addition, PIN-FORMED (PIN) transcripts were expressed differentially throughout the whole AR development process, with the up-regulation ofMdPIN8andMdPIN10during induction, an up-regulation ofMdPIN4,MdPIN5andMdPIN8during extension, and an up-regulation of allMdPINsduring AR initiation. This research provides a deeper understanding of the cellular and molecular underpinnings of the AR process in woody plants.
Solvent-triggered single-crystal-to-single-crystal transformation from a monomeric to polymeric copper(II) complex based on an aza macrocyclic ligand
Authors: Shin Jong Won , Jeong Ah Rim , Kim Younghak , Kim Dae-Woong , Lee Sang-Geul , Lee Hyosun , Moon Dohyun
Published: March 2020

Reversible solvent-triggered single-crystal-to-single-crystal (SCSC) transformations are observed between two copper(II) azamacrocyclic complexes: [Cu(C16H38N6)(H2O)2](C12H6O4) (1) and [Cu(C16H38N6)(C12H6O4)] (2). Complex (1) was prepared via self-assembly of a copper(II) azamacrocyclic complex containing butyl pendant groups, [Cu(C16H38N6)(ClO4)2], with 2,7-naphthalenedicarboxylic acid. When monomeric compound (1) was immersed in CH3OH, coordination polymer (2) was obtained, indicating a solvent-triggered SCSC transformation. Furthermore, when (2) was immersed in water, an reverse SCSC transformation from (2) to (1) occurred. Complex (1) presents a 3D supramolecular structure formed via intermolecular hydrogen-bonding interactions, whereas complex (2) features a 1D zigzag coordination polymer. The reversible SCSC transformation of (1) and (2) was characterized using single-crystal X-ray diffraction and in situ powder X-ray diffraction techniques. Despite its poor porosity, complex (2) displayed interesting CO2 adsorption behaviour under CO2 gas.
Effect of growth modes on electrical and thermal transport of thermoelectric ZnO:Al films
Authors: Liu Shiying , Li Guojian , Lan Mingdi , Piao Yongjun , Miyazaki Koji , Wang Qiang
Published: March 2020

Electrical and thermal transport controlled by growth mode can be used to optimize thermoelectric properties of ZnO:Al films, which was adjusted by the re-evaporation of Zn and Al via substrate temperatures. The growth modes include equiaxed crystal, columnar crystal and coexistence of both crystals. In the ZnO:Al film, equiaxed crystals improve the carrier mobility and reduce the lattice thermal conductivity. Thus, the carrier mobility and thermal conductivity are tuned by the ratio of equiaxed crystals to columnar crystals. The carrier mobility is dependent on the growth-mode-related defects of oxygen vacancies, zinc interstitials and the substitutional dopant of Al. Improved thermoelectric properties with a power factor of 198.45 µW m−1 K−2 at 510 K were achieved. This study presents a film with the structure of an equiaxed-crystal buffer layer to enhance its thermoelectric properties.
Growth of c-plane and m-plane aluminium-doped zinc oxide thin films: epitaxy on flexible substrates with cubic-structure seeds
Authors: Li Yongkuan , Liu Xinxing , Wen Dan , Lv Kai , Zhou Gang , Zhao Yue , Xu Congkang , Wang Jiangyong
Published: March 2020

Manufacturing high-quality zinc oxide (ZnO) devices demands control of the orientation of ZnO materials due to the spontaneous and piezoelectric polarity perpendicular to the c-plane. However, flexible electronic and optoelectronic devices are mostly built on polymers or glass substrates which lack suitable epitaxy seeds for the orientation control. Applying cubic-structure seeds, it was possible to fabricate polar c-plane and nonpolar m-plane aluminium-doped zinc oxide (AZO) films epitaxially on flexible Hastelloy substrates through minimizing the lattice mismatch. The growth is predicted of c-plane and m-plane AZO on cubic buffers with lattice parameters of 3.94–4.63 Å and 5.20–5.60 Å, respectively. The ∼80 nm-thick m-plane AZO film has a resistivity of ∼11.43 ± 0.01 × 10−4 Ω cm, while the c-plane AZO film shows a resistivity of ∼2.68 ± 0.02 × 10−4 Ω cm comparable to commercial indium tin oxide films. An abnormally higher carrier concentration in the c-plane than in the m-plane AZO film results from the electrical polarity along the c-axis. The resistivity of the c-plane AZO film drops to the order of 10−5 Ω cm at 500 K owing to the semiconducting behaviour. Epitaxial AZO films with low resistivities and controllable orientations on flexible substrates offer optimal transparent electrodes and epitaxy seeds for high-performance flexible ZnO devices.
Corporate governance and underpricing of small and medium enterprises IPOs in India
Authors: Arora Nischay , Singh Balwinder
Published: March 2020

Purpose

The purpose of the paper is to examine the impact of corporate governance mechanisms, i.e. board structure and ownership structure on the underpricing of small and medium enterprises (SME) IPOs in India.

Design/methodology/approach

Most of the extant empirical research studies have either pivoted on mainstream IPOs or SMEs IPOs in developed economies, but the present study examines 200 SME IPOs issued during Feb 2012 to April 2017. Multiple regressions have been used to examine the impact of the corporate governance mechanisms on raw return (RR). Furthermore, robustness of the results has been verified through the employment of market-adjusted excess return (MAER) as an additional proxy of underpricing.

Findings

The results highlight that board size, inverse of board committees, board independence, board age, board directorships positively, and top ten shareholding negatively influence RR. Further, direction of promoter ownership variable indicates curvilinear relationship with underpricing. Other explanatory variables used in model lack statistical validity. Similar results have been obtained when variables were regressed against MAER with related board members being additionally significant in model.

Practical implications

The findings suggest that Indian investors do take cues from board structure and ownership patterns for making investment decisions in small- and medium-sized firms. Further, the results are also helpful to top management in structuring their boards.

Originality/value

The present research enriches SME IPOs underpricing literature because the impact of corporate governance mechanisms on unadjusted returns is relatively under explored particularly within the context of small- and medium-sized firms.
Product development in Islamic finance and banking in secular economies
Authors: Dinc Yusuf
Published: March 2020

Purpose

As the global paradigm in economics shifts, Islamic economics is attracting more attention as an alternative sector. The most common and most active institutional structure of Islamic economics is in the form of Islamic finance and banking. Islamic finance and banking have been the centre of innovation in many economies in recent years. In this regard, product development is a vital element in driving the success of Islamic financial institutions (IFIs). The product development of IFIs is one of the key elements of their overall economic performance. This study aims to fill the gap in the literature concerning the product development process of IFIs in secular economies.

Design/methodology/approach

Verily, product development is a complex process; it is likely that introducing specific models will be useful for expanding the activities of IFIs. In this study, contemporary source materials are used to develop this conceptual research.

Findings

It suggests two separate methodologies for the product development process of IFIs in secular economies to overhaul two criticised product-based problems. To the best of the author’s knowledge, it is the first attempt to model the product development process for IFIs in a secular economic setup.

Originality/value

Recently, this study is the first attempt for modelling product development in IFIs under secular economies. Advances in the field of Shari’ah-compliant product development is important for researchers and professional.
Shopping value, trust, and online shopping well-being: a duality approach
Authors: Nghia Ho Trong , Olsen Svein Ottar , Trang Nguyen Thi Mai
Published: March 2020

Purpose

Based on a duality approach, this study examines the path from utilitarian value via cognitive trust versus hedonic value via affective trust in online shopping well-being. This study also explores the moderating role of extraversion in the relationships between shopping value and trust.

Design/methodology/approach

A data set collected from 648 online consumers in Vietnam was used to validate the measures employing confirmatory factor analysis (CFA) and to test the hypotheses using structural equation modelling (SEM).

Findings

The results show that online shopping well-being is determined hedonically and affectively rather than in an utilitarian manner and cognitively. Affective trust positively contributes to online shopping well-being, but cognitive trust does not. The dual-process associations between utilitarian shopping value and cognitive trust and between hedonic shopping value and cognitive trust were also confirmed. Finally, extraversion moderates the cognitive and affective associations between shopping values and trust.

Originality/value

This study contributes to the literature on online shopping by applying a dual perspective to confirm the role of hedonic shopping value and affective trust in positively determining online shopping well-being. As a result, this study provides a deeper understanding about if and why online shopping well-being is affect-based, instead of cognition-based.
A novel dimethylsulfoxide reductase family of molybdenum enzyme, Idr, is involved in iodate respiration by Pseudomonas sp. SCT
Authors: Yamazaki Chihiro , Kashiwa Sumie , Horiuchi Ayaka , Kasahara Yasuhiro , Yamamura Shigeki , Amachi Seigo
Published: March 2020

Pseudomonas sp. strain SCT is capable of using iodate (IO3−) as a terminal electron acceptor for anaerobic respiration. A possible key enzyme, periplasmic iodate reductase (Idr), was visualized by active staining on non‐denaturing gel electrophoresis. Liquid chromatography–tandem mass spectrometry analysis revealed that at least four proteins, designated as IdrA, IdrB, IdrP1, and IdrP2, were involved in Idr. IdrA and IdrB were homologues of catalytic and electron transfer subunits of respiratory arsenite oxidase (Aio); however, IdrA defined a novel clade within the dimethylsulfoxide (DMSO) reductase family. IdrP1 and IdrP2 were closely related to each other and distantly related to cytochrome c peroxidase. The idr genes (idrABP
1P
2) formed an operon‐like structure, and their transcription was upregulated under iodate‐respiring conditions. Comparative proteomic analysis also revealed that Idr proteins and high affinity terminal oxidases (Cbb3 and Cyd), various H2O2 scavengers, and chlorite (ClO2−) dismutase‐like proteins were expressed specifically or abundantly under iodate‐respiring conditions. These results suggest that Idr is a respiratory iodate reductase, and that both O2 and H2O2 are formed as by‐products of iodate respiration. We propose an electron transport chain model of strain SCT, in which iodate, H2O2, and O2 are used as terminal electron acceptors.
Testing the impact of financial inclusion on income convergence: Empirical evidence from Nigeria
Authors: Ibrahim Saifullahi Sani , Aliero Haruna Mohammad
Published: March 2020

Financial inclusion, as a key pillar for inclusive development, has long been considered as an important instrument for reducing poverty and income inequality. However, the income convergence effect of financial inclusion remains only partially explored. Using longitudinal data covering three survey waves on Nigerian households, this study explores the potential of financial inclusion as an instrument for reducing income disparity. After controlling for the endogeneity issues, the results of instrumental variable linear and quantile regressions consistently show a strong nexus between financial inclusion and per capita income. This positive effect is experienced by all households regardless of income distribution. The decomposition results reveal that ab initio, financial inclusion resulted in income divergence leading to widening inequality across the households with various income distributions. However, the income convergence started from the middle to the higher income household categories, with the lowest income lagging behind in the second wave. The lowest income households eventually converged in the data of the third wave. In this sense, it can be argued that financial inclusion could play an important role in the reduction of income inequality.
Estimation of the East African Community's trade benefits from promoting intra‐regional trade
Authors: Umulisa Yvonne
Published: March 2020

In the literature on economic integration, the optimum currency area (OCA) theory says that there should be a high degree of trade between potential members of a monetary union for them to benefit from the use of a single currency. This study uses an augmented gravity model of trade to estimate the East African Community's (EAC) trade effects, as this community decided to participate in a monetary union by 2024. The study uses the fixed effect filter (FEF) estimator, which follows a two‐step approach and outperforms the standard fixed effects (FE) estimator. The results indicate that EAC has the potential to increase trade among partner states by 122% more than expected from the normal trade levels. The study, therefore, supports the ongoing East African Monetary Union process. However, to improve the likelihood of creating a more sustainable monetary union, the study recommends these countries to primarily focus on the full implementation of the customs union and common market steps. The main contribution of this study is that it provides robust estimates of the EAC's effects on intra‐regional trade using more recent data and updated econometric techniques.
The (Re)Making of Polycentricity in China's Planning Discourse: The Case of Tianjin
Authors: Wang Weikai , Wang Ya Ping , Kintrea Keith
Published: March 2020

Polycentricity is promoted as an ideal urban form to achieve sustainable and balanced development, and it has been widely adopted by planners in China, especially in large cities. However, the rhetoric about polycentricity has rarely been interrogated in planning research in terms of scales, contextuality, power and rationality. To fill this gap, we carried out a Foucauldian discourse analysis in our research to interpret the nature of polycentric practice in City Master Plans, using Tianjin as a case study. Through an analysis of how the discourse of polycentricity is being deployed in planning documents, we develop two principal arguments in this article. First, the conceptual substance of polycentricity evolved alongside the urban transition process in China, and its discursive practice involved multiple scales and spatial elements. Secondly, rather than being mere technocratic practice, the production and legitimation of distinct discourses of polycentricity is an articulation of multi‐scalar power involving various stakeholders, which is disguised and justified by the planning profession.
Maternal risk factors and adverse birth outcomes associated with HELLP syndrome: a population‐based study
Authors: Lisonkova S , Razaz N , Sabr Y , Muraca GM , Boutin A , Mayer C , Joseph KS , Kramer MS
Published: March 2020

Objectives

We assessed the incidence, risk factors and adverse birth outcomes associated with elevated liver enzymes and low platelets (HELLP) syndrome.

Design

A retrospective population‐based cohort study.

Setting

Canada (excluding Quebec), 2012/2013–2015/2016.

Population

Mothers with a singleton hospital live birth or stillbirth at ≥24 weeks’ gestation (n = 1 078 323).

Methods

HELLP syndrome was identified using ICD‐10‐CA diagnostic code from delivery hospitalisation data. We used logistic regression to identify independent risk factors for HELLP syndrome by obtaining adjusted odds ratios (AOR) and 95% confidence intervals (CI), and to assess the associations with adverse outcomes.

Main outcome measures

Adverse maternal (e.g. eclampsia) and fetal/neonatal outcomes (e.g. intraventricular haemorrhage, perinatal death).

Results

The incidence of HELLP syndrome was 2.5 per 1000 singleton deliveries (n = 2663). Risk factors included: age ≥35 years, rural residence, nulliparity, parity ≥4, pre‐pregnancy and gestational hypertension and diabetes, assisted reproduction, chronic cardiac conditions, systemic lupus erythematosus, obesity, chronic hepatic conditions, placental disorders (e.g. fetomaternal transfusion) and congenital anomalies. PROM and age <25 years were inversely associated with HELLP syndrome (P‐values <0.05). Women with the syndrome had a 10‐fold higher maternal mortality (95% CI 1.6–84.3) and elevated severe maternal morbidity (9.6 versus 121.7 per 1000; AOR 12.5, 95% CI 11.1–14.1); and higher perinatal mortality (4.3 versus 21.0 per 1000; AOR 4.5, 95% CI 3.5–5.9) and perinatal mortality/severe neonatal morbidity (21.2 versus 202.4 per 1000; AOR 10.7, 95% CI 9.7–11.8).

Conclusion

HELLP syndrome is associated with specific pre‐pregnancy and pregnancy risk factors, higher rates of maternal death, and substantially higher severe maternal morbidity, perinatal mortality and severe neonatal morbidity.

Tweetable abstract

HELLP syndrome is associated with higher maternal death rate, and substantially higher severe maternal and neonatal morbidity, and perinatal mortality.
Real world study for the concordance between IBM Watson for Oncology and clinical practice in advanced non‐small cell lung cancer patients at a lung cancer center in China
Authors: Yao Shuyang , Wang Ruotian , Qian Kun , Zhang Yi
Published: March 2020

Background

IBM Watson for Oncology (WFO) provides physicians with evidence‐based treatment options. This study was designed to explore the concordance of the suggested therapeutic regimen for advanced non‐small cell lung (NSCLC) cancer patients between the updated version of WFO and physicians in our department, in order to reflect the differences of cancer treatment between China and the United States.

Methods

Retrospective data from 165 patients with advanced NSCLC from September 2014 to March 2018 were entered manually into WFO. WFO recommendations were provided in three categories: recommended, for consideration, and not recommended. Concordance was analyzed by comparing the treatment decisions proposed by WFO with the real treatment. Potential influenced factors were also analyzed.

Results

Overall, the treatment recommendations were concordant in 73.3% (121/165) of cases. When two alternative drugs such as icotinib and nedaplatin were included as “for consideration,” the total consistency could be elevated from 73.3% to 90.3%(149/165). The logistic regression analysis showed that gender (P = 0.096), ECOG (P = 0.0.502), smoking (P = 0.455), and pathology (P = 0.633) had no effect on consistency, but stages (P = 0.019), including stage ≤III (77.8%, 21/27) and stage IV (93.5%, 129/138) had significant effects on consistency.

Conclusions

In China, most of the treatment recommendations of WFO are consistent with the real world treatment. Factors such as patient preferences, prices, drug approval and medical insurance are also taken into consideration, and they ultimately affect the inconsistency. To be comprehensively and rapidly applied in China, localization needs to be accelerated by WFO.
Surgical effect and prognostic factors of myasthenia gravis with thymomas
Authors: Tian Wenxin , Li Xiao , Tong Hongfeng , Weng Wenhan , Yang Fan , Jiang Guanchao , Wang Jun
Published: March 2020

Background

To evaluate the surgical effect and prognostic factors of extended thymectomy for myasthenia gravis (MG) patients with thymomas.

Methods

Patients with MG with thymomas who underwent extended thymectomy at Peking University People's Hospital and Beijing Hospital between January 2010 and December 2018 were retrospectively enrolled. Patients were followed up by telephone or outpatient record review . Statistical analyses were performed using SPSS version 19.0.

Results

A total of 194 patients were included in this study. According to the Osserman classification, there were 56 type I, 52 type IIa, 67 type IIb, 14 type III, and five type IV. Video‐assisted thoracoscopic surgery (VATS) thymectomies were performed in 137 patients, and transthymectomies in 57 patients. The average operation time was 136.6 ± 46.5 minutes, average blood loss was 129.3 ± 287.4 mL, and average postoperative stay was 8.3 ± 7.4 days. A total of 170 patients (87.6%) were successfully followed up. The median follow‐up period was 45 months, and the five‐year overall survival (OS) rate was 81.9%. Cox regression analysis demonstrated that age, Masaoka stage, and recurrence were prognostic factors of OS. Tumor recurrence tended to occur in patients with Masaoka stage III + IV, and age was a protective factor. A total of 20 patients experienced postoperative myasthenic crisis (POMC). Univariate analysis indicated that presence of bulbar symptoms, surgical procedure, and blood loss were risk factors for POMC, but multivariate analysis only indicated the presence of bulbar symptoms as an independent risk factor. A total of 162 patients were evaluated for post intervention MG status. A total of 55 patients achieved complete stable remission; the overall effective rate was 84.5%. Older patients and those with B‐type thymomas had a lower probability of achieving complete stable remission. Efficacy was similar in patients who underwent VATS or the transsternal procedure.

Conclusions

Age, Masaoka stage, and recurrence were prognostic factors of OS. Presence of bulbar symptoms was an independent risk factor for POMC. Age and World Health Organization classification influence the postoperative effect of MG.

Key points

Significant findings of the study

Age, Masaoka stage, and recurrence were prognostic factors of OS for MG with thymomas. The presence of bulbar symptoms was an independent risk factor for POMC. Age and World Health Organization classification may influence the postoperative effect of MG.

What this study adds

Our study had a relatively large sample size of MG patients with thymomas only. We emphasize the analysis of the postoperative effect of MG and overall survival for these patients, which is a complement to previous studies.