bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiological measures for informing the general public during the SARS-CoV-2-outbreak: simulation study about bias by incomplete case-detection
Authors: Brinks Ralph , Küchenhoff Helmut , Timm Jörg , Kurth Tobias , Hoyer Annika
Published: September 2020

During the SARS-CoV-2 outbreak, several epidemiological measures, such as cumulative case-counts, incidence rates, effective reproduction numbers and doubling times, have been used to inform the general public and to justify interventions such as lockdown.

During the course of the epidemic, it has been very likely that not all infectious people have been identified, which lead to incomplete case-detection. Apart from asymptomatic infections, possible reasons for incomplete case-detection are availability of test kits and changes in test policies during the course of the epidemic. So far, it has not been examined how biased the reported epidemiological measures are in the presence of incomplete case detection.

In this work, we assess the four frequently used measures with respect to incomplete case-detection: 1) cumulative case-count, 2) incidence rate, 3) effective reproduction number and 4) doubling time. We apply an age-structured SIR model to simulate a SARS-CoV-2 outbreak followed by a lockdown in a hypothetical population. Different scenarios about temporal variations in case-detection are applied to the four measures during outbreak and lockdown. The biases resulting from incomplete case-detection on the four measures are compared. It turns out that the most frequently used epidemiological measure, the cumulative case count is most prone to bias in all of our settings. The effective reproduction number is the least biased measure.

With a view to future reporting about this or other epidemics, we recommend to use of the effective reproduction number for informing the general public and policy makers.
Using Histopathology Images to Predict Chromosomal Instability in Breast Cancer: A Deep Learning Approach
Authors: Xu Zhuoran , Verma Akanksha , Naveed Uska , Bakhoum Samuel , Khosravi Pegah , Elemento Olivier
Published: September 2020

Chromosomal instability (CIN) is a hallmark of human cancer that involves mis-segregation of chromosomes during mitosis, leading to aneuploidy and genomic copy number heterogeneity. CIN is a prognostic marker in a variety of cancers, yet, gold-standard experimental assessment of chromosome mis-segregation is difficult in the routine clinical setting. As a result, CIN status is not readily testable for cancer patients in such setting. On the other hand, the gold-standard for cancer diagnosis and grading, histopathological examinations, are ubiquitously available. In this study, we sought to explore whether CIN status can be predicted using hematoxylin and eosin (H&E) histology in breast cancer patients. Specifically, we examined whether CIN, defined using a genomic aneuploidy burden approach, can be predicted using a deep learning-based model. We applied transfer learning on convolutional neural network (CNN) models to extract histological features and trained a multilayer perceptron (MLP) after aggregating patch features obtained from whole slide images. When applied to a breast cancer cohort of 1,010 patients (Training set: n=858 patients, Test set: n=152 patients) from The Cancer Genome Atlas (TCGA) where 485 patients have high CIN status, our model accurately classified CIN status, achieving an area under the curve (AUC) of 0.822 with 81.2% sensitivity and 68.7% specificity in the test set. Patch-level predictions of CIN status suggested intra-tumor spatial heterogeneity within slides. Moreover, presence of patches with high predicted CIN score within an entire slide was more predictive of clinical outcome than the average CIN score of the slide, thus underscoring the clinical importance of spatial heterogeneity. Overall, we demonstrated the ability of deep learning methods to predict CIN status based on histopathology slide images. Our model is not breast cancer subtype specific and the method can be potentially extended to other cancer types.
Tuning TPO-R signaling to influence hematopoietic stem cell differentiation and inhibit essential thrombocythemia
Authors: Cui Lu , Moraga Ignacio , Lerbs Tristan , Neste Camille Van , Wilmes Stephan , Tsutsumi Naotaka , Trotman-Grant Aaron Claudius , Gakovic Milica , Andrews Sarah , Gotlib Jason , Darmanis Spyridon , Enge Martin , Quake Stephen , Hitchcock Ian S. , Piehler Jacob , Garcia K. Christopher , Wernig Gerlinde
Published: September 2020

Thrombopoietin (TPO) and the TPO-receptor (TPO-R, or c-MPL)) are essential for hematopoietic stem cell (HSC) maintenance and megakaryocyte differentiation. Agents that can modulate TPO-R signaling are highly desirable, both experimentally and clinically. We have developed a series of surrogate protein-ligands for TPO-R, in the form of diabodies, that homodimerize the TPO-R on the cell surface in different geometries, in effect ‘tuning’ downstream signaling responses. These surrogate ligands exhibit diverse pharmacological properties, inducing graded signaling outputs, from full to partial TPO agonism and antagonism, thus decoupling the dual functions of TPO/TPO-R. Using scRNA sequencing and HSC self-renewal assays we find that partial agonistic diabodies preserved the stem-like properties of cultured HSCs, but also blocked oncogenic colony formation in Essential Thrombocythemia (ET) through inverse agonism. Our data suggest that dampening downstream TPO signaling is a powerful approach not only for HSC preservation in culture, but also for inhibiting oncogenic signaling through the TPO-R.

Significance Statement

The TPO cytokine, which signals through its receptor c-MPL (or TPO-R), is essential for megakaryocyte differentiation and maintenance of hematopoietic stem cells (HSCs). Its signaling is deregulated in Essential Thrombocythemia (ET). Here, we engineered diabodies (DBs) against the TPO-R as surrogate TPO ligands to manipulate TPO-R signaling, from full to partial to antagonism, thus decoupling the dual functions of TPO/TPO-R (i.e, HSC maintenance versus megakaryopoiesis). We subsequently discovered that partial agonistic DBs, by reducing the strength of the TPO-R signal, not only preserved HSCs in culture, but also blocked oncogenic signaling in ET. This finding has the potential to improve HSC cultures for transplants, as well as serve as a unique therapeutic approach for ET.
Germline DNA replication shapes the recombination landscape in mammals
Authors: Pratto Florencia , Brick Kevin , Cheng Gang , Lam Gabriel , Cloutier Jeffrey M. , Dahiya Daisy , Wellard Stephen R. , Jordan Philip W. , Camerini-Otero R. Daniel
Published: September 2020

Genetic recombination generates novel trait combinations and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots, however megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns, therefore we devised a novel approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis and a distinctive replication pattern in human males underlies the sub-telomeric increase in recombination. We detected a robust correlation between replication and both contemporary and ancestral recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have far-reaching implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.
A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2
Authors: Zhang Li , Cao Lei , Gao Xing-Su , Zheng Bin-Yang , Deng Yong-Qiang , Li Jing-Xin , Feng Rui , Bian Qian , Guo Xi-Ling , Wang Nan , Qiu Hong-Ying , Wang Lei , Cui Zhen , Ye Qing , Chen Geng , Lu Kui-Kui , Chen Yin , Chen Yu-Tao , Pan Hong-Xing , Zhu Bao-Li , Qin Cheng-Feng , Wang Xiangxi , Zhu Feng-Cai
Published: September 2020

Mutations and transient conformational movements of receptor binding domain (RBD) that make neutralizing epitopes momentarily unavailable, present immune escape routes to SARS-CoV-2. To mitigate viral escape, we developed a cocktail of neutralizing antibodies (NAbs) targeting epitopes located on different domains of spike (S) protein. Screening of a library of monoclonal antibodies generated from peripheral blood mononuclear cells of COVID-19 convalescent patients yielded potent NAbs, targeting N-terminal domain (NTD) and RBD domain of S, effective atnMconcentrations. Remarkably, combination of RBD-targeting NAbs and NTD-binding NAb, FC05, dramatically enhanced the neutralization potency in cell-based assays and animal model. Results of competitive SPR assays and cryo-EM structures of Fabs bound to S unveil determinants of immunogenicity. Combinations of immunogens, identified in NTD and RBD of S, when immunized in rabbits elicited potent protective immune responses against SARS-CoV-2. These results provide a proof-of-concept for neutralization-based immunogen design targeting SARS-CoV-2 NTD and RBD.

One sentence summary

Immunogens identified in the NTD and RBD of the SARS-CoV-2 spike protein using a cocktail of non-competing NAbs when injected in rabbits elicited a potent protective immune response against SARS-CoV-2.
A first-takes-all model of centriole copy number control
Authors: Dias Louro Marco António , Bettencourt-Dias Mónica , Carneiro Jorge
Published: September 2020

How cells control the numbers of its subcellular components is a fundamental question in biology. Given that biosynthetic processes are fundamentally stochastic it is utterly puzzling that some structures display no copy number variation within a cell population. Centriole biogenesis, with each centriole being duplicated once and only once per cell cycle, stands out due to its remarkable fidelity. This is a highly controlled process, which depends on low-abundance rate-limiting factors. How can exactly one centriole copy be produced given the natural variation in the concentration of these key players? Hitherto, tentative explanations of this control evoked lateral inhibition-or phase separation-like mechanisms emerging from the dynamics of these rate-limiting factors, but how centriole number is regulated remains unclear. Here, we propose a novel solution to centriole copy number control based on the assembly of a centriolar scaffold, the cartwheel. We hypothesise that once the first cartwheel is formed it continues to elongate by stacking the intermediate cartwheel building blocks that would otherwise form supernumerary structures. Using probability theory and computer simulations, we show that this mechanism may ensure formation of one and only one cartwheel over a wide range of parameter values at physiologically relevant conditions. By comparison to alternative models, we conclude that the key signatures of this novel mechanism are an increasing assembly time with cartwheel numbers and that stochasticity in cartwheel building blocks should be converted into variation in cartwheel numbers or length, both of which can be tested experimentally.

Author summary

Centriole duplication stands out as a biosynthetic process of exquisite fidelity in the noisy world of the cell. Each centriole duplicates exactly once per cell cycle, such that the number of centrioles per cell shows no variance across cells, in contrast with most cellular components that show broadly distributed copy numbers. We propose a new solution to the number control problem. We show that elongation of the first cartwheel, a core centriolar structure, may sequester the building blocks necessary to assemble supernumerary centrioles. As a corollary, the variation in regulatory kinases and cartwheel components across the cell population is predicted to translate into cartwheel length variation instead of copy number variation, which is an intriguing overlooked possibility.
PspA adopts an ESCRT-III-like fold and remodels bacterial membranes
Authors: Junglas Benedikt , Huber Stefan T. , Heidler Thomas , Schlösser Lukas , Mann Daniel , Hennig Raoul , Clarke Mairi , Hellmann Nadja , Schneider Dirk , Sachse Carsten
Published: September 2020

PspA is the main effector of the phage shock protein (Psp) system and preserves the bacterial inner membrane integrity and function. Here, we present the 3.6 Å resolution cryo-EM structure of PspA assembled in helical rods. PspA monomers adopt a canonical ESCRT-III fold in an extended open conformation. PspA rods are capable of enclosing lipids and generate positive membrane curvature. Using cryo-EM we visualized how PspA remodels membrane vesicles into μm-sized structures and how it mediates the formation of internalized vesicular structures. Hot spots of these activities are zones derived from PspA assemblies, serving as lipid transfer platforms and linking previously separated lipid structures. These membrane fusion and fission activities are in line with the described functional properties of bacterial PspA/IM30/LiaH proteins. Our structural and functional analyses reveal that bacterial PspA belongs to the evolutionary ancestry of ESCRT-III proteins involved in membrane remodeling.
Co-Citation Percentile Rank and JYUcite: a new network-standardized output-level citation influence metric and its implementation using Dimensions API
Authors: Seppänen Janne-Tuomas , Värri Hanna , Ylönen Irene
Published: September 2020

Judging value of scholarly outputs quantitatively remains a difficult but unavoidable challenge. Most of the proposed solutions suffer from three fundamental shortcomings: they involve i) the concept of journal, in one way or another, ii) calculating arithmetic averages from extremely skewed distributions, and iii) binning data by calendar year. Here, we introduce a new metric Co-citation Percentile Rank (CPR), that relates the current citation rate of the target output taken at resolution of days since first citable, to the distribution of current citation rates of outputs in its co-citation set, as its percentile rank in that set. We explore some of its properties with an example dataset of all scholarly outputs from University of Jyväskylä spanning multiple years and disciplines. We also demonstrate how CPR can be efficiently implemented with Dimensions database API, and provide a publicly available web resource JYUcite, allowing anyone to retrieve CPR value for any output that has a DOI and is indexed in the Dimensions database. Finally, we discuss how CPR remedies failures of the Relative Citation Ratio (RCR), and remaining issues in situations where CPR too could potentially lead to biased judgement of value.
Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe
Authors: Katz Ella , Bagaza Clement , Holden Samuel , Angelovici Ruthie , Kliebenstein Daniel J.
Published: September 2020

Plants face a variety of challenges within their ever-changing environment. Diverse metabolites are central to the plants ability to overcome these challenges. Understanding the environmental and genetic factors influencing the variation in specialized metabolites is the key to understand how plants survive and develop under changing environments. Here we measure the variation in specialized metabolites across a population of 797 naturalArabidopsis thalianaaccessions. We show a combination of geography, environmental parameters, demography, and different genetic processes that creates a specific pattern in their accumulation and distribution. By identifying and tracking causal polymorphisms at multiple loci controlling metabolites variation we show that each locus displays extensive allelic heterogeneity with signatures of both parallel and convergent evolutionary processes. These loci combine epistatically and show differing relationships to environmental parameters leading to different distributions. This provides a detailed perspective about the complexity of the forces and mechanisms that shape the accumulation and distribution of a family of specialized metabolites critical for plant fitness.
Heteroplasmy and repeat expansion in the plant-like mitochondrial genome of a bivalve mollusc
Authors: Calcino Andrew , Baranyi Christian , Wanninger Andreas
Published: September 2020

Background

Animal mitochondrial genomes are typically circular, 14-20 kb in length, maternally inherited, contain 13 coding genes, two ribosomal genes and are homoplasmic. In contrast, plant mitogenomes display frequent gene rearrangements, often contain greatly expanded repetitive regions, encode various open reading frames of unknown function and may be heteroplasmic due to differential repeat expansions between molecules. Error correction by recombination is common in plant mitochondria and has been proposed as the driver behind the rearrangements and repeat expansions that are often observed. In contrast, most animal mitochondria never or only very seldomly recombine and their utilisation of other repair mechanisms for mitochondrial genome error correction is a potential driver of their non-coding DNA reduction.

Results

Using PacBio long reads for genome assembly and structural variant detection, we identify evidence of heteroplasmy in the form of variable repeat lengths within two blocks of repetitive DNA within the expanded 46 kb mitochondrial genome of the bivalve mollusc, quagga mussel,Dreissena rostriformis. The quagga mussel also has a greatly expanded repertoire of coding genes in comparison to most animals which includes an additional nine open reading frames (ORFs) encoding predicted transmembrane peptides of unknown orthology.

Conclusions

The genome size, repeat content and coding gene repertoire of the quagga mussel mitogenome closely resemble those of plants and the identification of repeat-associated heteroplasmy is consistent with the utilisation of plant-like recombination-based error correction mechanisms. Given the frequency of mitochondrial repeat expansions within the Bivalvia, recombination may be an underappreciated mechanism for mitogenomic error correction within this and other animal lineages.

Significance Statement

Unlike most animals, the mitochondrial genomes of many bivalve molluscs are often greatly expanded and contain large non-coding regions and additional predicted genes of unknown function. While these features are uncommon in other animal groups, they are common features of plant mitochondrial genomes. Here we show that the mitochondrial genome of the bivalve mollusc, the quagga mussel, displays many plant-like features and additionally, shows evidence of variability in the repeat lengths between mitochondrial molecules within an individual mussel. We propose that similar error correction mechanisms in plants and bivalves may play a role in these observed commonalities.
Cross kingdom analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets to ameliorate fungal pathogenicity?
Authors: Warner Emily F. , Bohálová Natália , Brázda Václav , Waller Zoë A. E. , Bidula Stefan
Published: September 2020

Fungi contribute to upwards of 1.5 million human deaths annually, are involved in the spoilage of up to a third of food crops, and have a devastating effect on plant and animal biodiversity. Moreover, this already significant issue is exacerbated by a rise in antifungal resistance and a critical requirement for novel drug targets. Quadruplexes are four-stranded secondary structures in nucleic acids which can regulate processes such as transcription, translation, replication, and recombination. They are also found in genes linked to virulence in microbes, and quadruplex-binding ligands have been demonstrated to eliminate drug resistant pathogens. Using a computational approach, we identified putative quadruplex-forming sequences (PQS) in 1362 genomes across the fungal kingdom and explored their potential involvement in virulence, drug resistance, and pathogenicity. Here we present the largest analysis of PQS in fungi and identified significant heterogeneity of these sequences throughout phyla, genera, and species. Moreover, PQS were genetically conserved. Notably, loss of PQS in cryptococci and aspergilli was associated with pathogenicity. PQS in the clinically important pathogensAspergillus fumigatus, Cryptococcus neoformans, andCandida albicanswere located within genes (particularly coding regions), mRNA, repeat regions, mobile elements, tRNA, ncRNA, rRNA, and the centromere. Genes containing PQS in these organisms were found to be primarily associated with metabolism, nucleic acid binding, transporter activity, and protein modification. Finally, PQS were found in over 100 genes associated with virulence, drug resistance, or key biological processes in these pathogenic fungi and were found in genes which were highly upregulated during germination, hypoxia, oxidative stress, iron limitation, and in biofilms. Taken together, quadruplexes in fungi could present interesting novel targets to ameliorate fungal virulence and overcome drug resistance.
Correlating the structure and activity ofY. pestisAil in a bacterial cell envelope
Authors: Kent J. E. , Fujimoto L. M. , Shin K. , Singh C. , Yao Y. , Park S. , Opella S. J. , Plano G. V. , Marassi F. M.
Published: September 2020

Understanding microbe-host interactions at the molecular level is a major goal of fundamental biology and therapeutic drug development. Structural biology strives to capture biomolecular structures in action, but the samples are often highly simplified versions of the complex native environment. Here we present anE. colimodel system that allows us to probe the structure and function of Ail, the major surface protein of the deadly pathogenYersinia pestis.We show that cell surface expression of Ail producesY. pestisvirulence phenotypes inE. coli,including resistance to human serum, co-sedimentation of human vitronectin and pellicle formation. Moreover, isolated bacterial cell envelopes, encompassing inner and outer membranes, yield high-resolution solid-state nuclear magnetic resonance (NMR) spectra that reflect the structure of Ail and reveal Ail sites that are sensitive to the bacterial membrane environment and involved in the interactions with human serum components. The data capture the structure and function of Ail in a bacterial outer membrane and set the stage for probing its interactions with the complex milieu of immune response proteins present in human serum.

SIGNIFICANCE

Ail is a critical virulence factor ofY. pestis,and its interactions with human serum are central for promoting the immune resistance of bacteria to the human host defenses. Here we capture the action of Ail in a functional bacterial environment and set the stage for probing its interactions with the complex milieu of immune response proteins present in human serum. The development of anE. colimodel system ofY. pestisfor biophysical studies is new and biologically important. Finally, the work extends the rangein-situNMR spectroscopy to include models of microbial infection.
Glycine acylation and trafficking of a new class of bacterial lipoprotein by a composite secretion system
Authors: Icke Christopher , Hodges Freya J. , Puella Karthik , McKeand Samantha A. , Bryant Jack A. , Cunningham Adam F. , Cole Jeff A. , Henderson Ian R.
Published: September 2020

Protein acylation is critical for many cellular functions including signal transduction, cell division and development. In bacteria, such lipoproteins have important roles in virulence and are therefore potential targets for the development of novel antimicrobials and vaccines. To date, all known bacterial lipoproteins are secreted from the cytosol via the Sec pathway, acylated on an N-terminal cysteine residue through the action of Lgt, Lsp and Lnt, and then targeted to the appropriate cellular location. In the case of Gram-negative bacteria, the lipoprotein trafficking Lol pathway transports the lipoproteins to the outer membrane where most substrate molecules are retained within the cell. Here we identify a new secretion pathway that displays the substrate lipoprotein on the cell surface. We demonstrate that the previously identifiedE. coliAat secretion system is a composite system that shares similarity with type I secretion systems and elements of the Lol pathway. Remarkably, during secretion by the Aat system, the AatD subunit acylates the substrate CexE on a highly conserved N-terminal glycine residue (rather than the canonical cysteine). Mutations in AatD or CexE that disrupt glycine acylation interfere with membrane incorporation and trafficking. Our data suggest that CexE is the first member of a new class of glycine-acylated bacterial lipoprotein, while Aat represents a new secretion system that we propose be defined as a lipoprotein secretion system (LSS).
Highly pathogenic avian influenza (H5N1) landscape suitability varies by wetland habitats and the degree of interface between wild waterfowl and poultry in India
Authors: Walsh Michael G. , Mor Siobhan M. , Hossain Shah
Published: September 2020

Highly pathogenic avian influenza (HPAI), subtype H5N1, constitutes one of the world’s most important health and economic concerns given the catastrophic impact of epizootics on the poultry industry, the high mortality attending spillover in humans, and its potential as a source subtype for a future pandemic. Nevertheless, we still lack an adequate understanding of HPAI H5N1 epidemiology and infection ecology. The nature of the wild waterfowl-poultry interface, and the sharing of diverse wetland habitat among these birds, currently underscore important knowledge gaps. India has emerged as a global hotspot for HPAI H5N1, while also providing critical wintering habitat for many species of migratory waterfowl and year-round habitat for several resident waterfowl species. The current study sought to examine the extent to which the wild waterfowl-poultry interface, varied wetland habitat, and climate influence HPAI H5N1 epizootics in poultry in India. Using World Organisation for Animal Health reported outbreaks, this study showed that the wild waterfowl-poultry interface and lacustrine, riparian, and coastal marsh wetland systems were strongly associated with landscape suitability, and these realtionships varied by scale. Although increasing poultry density was associated with increasing risk, this was only the case in the absence of wild waterfowl habitat, and only at local scale. In landscapes increasingly shared between wild waterfowl and poultry, suitability was greater among lower density poultry, again at local scale only. These findings provide further insight into the occurrence of HPAI H5N1 in India and suggest important landscape targets for blocking the waterfowl-poultry interface to interrupt virus transmission and prevent future outbreaks.
Evaluation method of ecosystem service value under complex ecological environment: A case study of Gansu Province, China
Authors: Zhao Xiaojiong , Wang Jian , Su Junde , Sun Wei
Published: September 2020

Scientific assessment of regional ecosystem service value (ESV) is helpful to make scientific ecological protection plan and compensation policy. The evaluation method has not been established that is adapted to the complex and diverse characteristics of the ecological environment. This paper takes Gansu Province as an example, on the basis of fully considering the regional differences of ecosystem service function, the five correction index of value equivalent factor per unit area were constructed in the provincial scale, and the regional difference adjustment index of 11 kinds of ES was constructed in regional scale, in the way, the value evaluation model based on regional difference was established. The results show that in 2015, the total ESV reached 2239.555 billion Yuan in Gansu Province, ESV gradually increased from the northeast to the southwest, and the high-value areas of service function located in Qilian Mountain and Longnan Mountain, of which the forest and grassland ecosystem contributed the most to the value. From the perspective of value composition, local climate regulation and biodiversity maintenance function are the main service functions of Gansu Province. From 2000 to 2015, ESV increased by 3.426 billion Yuan in Gansu Province, the value of forest and urban ecosystem continued increasing, while the value of cultivated land ecosystem continue decreasing. From the spatial characteristics of service value change, the area of value reduction gradually moved from the central part of Gansu Province to the surrounding area. In general, although this study needs further improvement, the constructed evaluation method provides a relatively comprehensive evaluation scheme for the spatiotemporal dynamic evaluation of ESV in Gansu Province. This study provided a more overall research idea for the evaluation of ESV under complex ecological environment.
Neural correlates of auditory pattern learning in the auditory cortex
Authors: Kang H. , Auksztulewicz R. , An H. J. , Abichacra N. , Sutter M. L. , Schnupp J. W. H.
Published: September 2020

Learning of new auditory stimuli requires repetitive exposure to the stimulus. Fast and implicit learning of sounds presented at random times enables efficient auditory perception. However, it is unclear how such sensory encoding is processed on a neural level. We investigated neural responses that are developed from a passive, repetitive exposure to a specific sound in the auditory cortex of anesthetized rats, using electrocorticography. We presented a series of random sequences that are generated afresh each time, except for a specific reference sequence that remains constant and re-appears at random times across trials. We compared induced activity amplitudes between reference and fresh sequences. Neural responses from both primary and non-primary auditory cortical regions showed significantly decreased induced activity amplitudes for reference sequences compared to fresh sequences, especially in the beta band. This is the first study showing that neural correlates of auditory pattern learning can be evoked even in anesthetized, passive listening animal models.
Agonist-induced functional analysis and cell sorting associated with single-cell transcriptomics characterizes cell subtypes in normal and pathological brain
Authors: Castagnola Sara , Cazareth Julie , Lebrigand Kevin , Jarjat Marielle , Magnone Virginie , Delhaye Sébastien , Brau Frederic , Bardoni Barbara , Maurin Thomas
Published: September 2020

To gain better insight into the dynamic interaction between cells and their environment, we developed the agonist-induced functional analysis and cell sorting (aiFACS) technique, which allows the simultaneous recording and sorting of cells in real-time according to their immediate and individual response to a stimulus. By modulating the aiFACS selection parameters, testing different developmental times, using various stimuli, and multiplying the analysis of readouts, it is possible to analyze cell populations of any normal or pathological tissue. The association of aiFACS with single-cell transcriptomics allows the construction of functional tissue cartography based on specific pharmacological responses of cells. As a proof of concept, we used aiFACS on the dissociated mouse brain, a highly heterogeneous tissue, enriching it in interneurons by stimulation with KCl or with AMPA, an agonist of the glutamate receptors, followed by sorting based on calcium levels. After AMPA stimulus, single-cell transcriptomics of these aiFACS-selected interneurons resulted in a nine-cluster classification. Furthermore, we used aiFACS on interneurons derived from the brain of the Fmr1-KO mouse, a rodent model of fragile X syndrome. We showed that these interneurons manifest a generalized defective response to AMPA compared with wild-type cells, affecting all the analyzed cell clusters at one specific postnatal developmental time.
Crystal structures and phase transitions of imidazolium hypodiphosphates
Authors: Budzikur Daria , Szklarz Przemysław , Kinzhybalo Vasyl , Ślepokura Katarzyna A.
Published: September 2020

Two imidazolium hypodiphosphates, (C3H5N2)(H3P2O6) (I) and (C3H5N2)2(H2P2O6) (II), have been synthesized and structurally characterized. In both metal-free organic–inorganic hybrids (I) and (II), the hypodiphosphate mono- and dianions, (H3P2O6)− and (H2P2O6)2−, form hydrogen-bonded frameworks of different types, to which the organic cations are linked via N—H...O and C—H...O hydrogen bonds. The purity of the compounds was confirmed by powder X-ray diffraction. Differential scanning calorimetry of compound (I) revealed two structural phase transitions: continuous at 311.8 K [cooling/heating; from high-temperature phase (HTP) to room-temperature phase (RTP)] and a discontinuous one at 287.9/289.2 K [RTP → low-temperature phase (LTP)]. Compound (I) is characterized in a wide temperature range by single-crystal and powder X-ray diffraction methods. Crystal structures of high- and low-temperature phases are determined, which show orthorhombic (HTP, Pnna, No. 52) → monoclinic (LTP, P21/n11, No. 14, a-axis doubled) structural change on cooling with an intermediate incommensurately modulated phase (RTP). Dynamic properties of polycrystalline (I) were studied by means of dielectric spectroscopy. The dielectric behaviour is explained by the motion of imidazolium cations.
An assessment of the financial soundness of the Kazakh banks
Authors: Salina Aigul P. , Zhang Xin , Hassan Omaima A.G.
Published: September 2020

Purpose

The contribution of the banking industry to the financial crisis of 2007/8 has raised public concerns about the financial soundness of banks around the world with many countries still suffering the backlogs of this crisis. The continuous emergence of such crises at both national and international levels increases governments', bank regulators' and financial market participants' need for reliable tools to assess the financial soundness of banks. In this context, this study investigates the financial soundness of the Kazakh banking sector, which is ranked by the World Bank as the first in the world in terms of the percentage of nonperforming loans (NPL) to total gross loans in 2012.

Design/methodology/approach

Using data about all Kazakh banks over the period January 01, 2008 to January 01, 2014, the study identifies a number of accounting indicators that influence the financial soundness of banks using principal component analysis (PCA). Then, it uses the outcomes of the PCA in a cluster analysis and groups the Kazakh banks into sound, risky and unsound banks at two points in time: January 01, 2008 and January 01, 2014. This methodology was further tested against a ranking system of banks and proved to be more reliable in detecting risky banks.

Findings

Fifteen financial ratios were initially selected as accounting indicators for the assessment of bank financial soundness. Using PCA, twelve indicators were isolated, which explain five principal components of capital adequacy, return on assets, profitability, asset quality, liquidity and leverage. Then using the “k-means” method, the results suggest a structure of the Kazakh banking sector on January 01, 2008 that includes two groups of banks: sound and risky banks. On January 01, 2014, this structure of the banking system has changed to include three groups of banks: sound, risky and unsound banks. Thus, in 2014 a new group of banks has emerged, i.e. financially unsound banks.

Practical implications

The proposed cluster-based methodology has proven to be a reliable tool to detect the financial soundness of Kazakh banks, which makes us advocate its employability for bank monitoring and supervision purposes.

Originality/value

This study is the first to employ a cluster-based methodology to assess the financial soundness of a banking sector. This methodology can be used at a micro-level to determine the structure of a banking sector. Also, it can be used to monitor any changes in the structure of a banking sector and provide early warning signals about the financial health of banks.
Spillover effects in the financial year cycle for Indian markets
Authors: Bhatia Parul
Published: September 2020

Purpose

The stock market anomalies have been studied across the globe with intermingled results for individual markets. The present study has investigated the financial year effect for Indian stock markets by testing month-of-the-year-effect anomalies.

Design/methodology/approach

The oldest stock exchange's index returns (Bombay Stock Exchange [BSE]) have been tested using ordinary least squares (OLS) and autoregressive conditional heteroskedasticity in mean (ARCH-M) models with Student's t and Student's t-fixed distributions for the period between 1991 and 2019. The Glosten, Jagannathan and Runkle-generalised autoregressive conditional heteroskedasticity (GJR-GARCH) model has been further used to find out existence of the leverage effect in returns.

Findings

The findings indicated no evidence for anomalies in the Indian stock market which may be used by investors for making unusual returns. However, the volatility in returns has shown weak but significant results due to the financial year impact. The leverage effect has not been found in the financial year cycle change over. The Indian market may be said to be moving towards a state of efficiency, leaving no scope for investors to gauge bizarre profits.

Research limitations/implications

The study has incorporated the Indian context for testing anomalies during the start and end of the financial year cycle. The model may be extended further to developed and developing nations’ markets for testing efficiency in their stock markets during the same cycle.

Originality/value

The paper may be the first of its kind to test for the financial year effect on standalone basis for Indian markets. The paper also adds to the existing literature on testing events’ effect.
The impact of foreign capital shifts on economic activities and asset prices: a threshold VAR approach
Authors: Baba Boubekeur , Sevil Güven
Published: September 2020

Purpose

The purpose of this paper is to investigate the impact of foreign capital shifts on economic activities and asset prices in South Korea.

Design/methodology/approach

The authors in this paper apply the Bayesian threshold vector autoregressive (TVAR) model to estimate the regimes of large and low inflows of foreign capital. Then, structural impulse-response analysis is used to check whether the responses of the variables differ across the estimated regimes. The model is estimated using quarterly data of foreign capital inflows, gross domestic product (GDP), consumer price index, credit to the private non-financial sector, real effective exchange rate (REER), stock returns and house prices.

Findings

The main findings suggest that large inflows of gross foreign capital, foreign direct investments (FDI) and foreign portfolio investments (FPI) are ineffective to boost economic growth, but large inflows of other foreign investments (OFIs) significantly contribute to GDP. The decreases in the foreign capital inflows are associated with larger depreciation of REER. The large inflows of gross foreign capital, FDI and OFIs are associated with further expansion of credit supply to private non-financial sectors.

Research limitations/implications

The policy implications of foreign capital inflows are of particular importance to all the emerging markets alike. However, the empirical analysis is limited to the case of South Korea due to various reasons. The experience with international capital inflows among emerging markets is heterogeneous. Therefore, it would be better to take each case of emerging market individually. In addition, TVAR analysis requires a long data sample, which unfortunately is not available for most of the emerging markets.

Originality/value

The foreign capital inflows are shown to be procyclical and notoriously volatile in many studies. Nevertheless, this topic has commonly been studied using linear VAR models, which do not properly deal with the cyclical characteristics of foreign capital inflows. This study attempts to resolve these methodological limitations by examining a non-linear VAR model that is capable of capturing the structural breaks associated with the cyclical behaviors of foreign capital inflows.
Discrepancy in oil film distribution observed in ZEV reciprocating motion
Authors: Jin Xuyang , Wang Jing , Han Yiming , Sun Nannan , Zhu Jianrong
Published: September 2020

Purpose

This study aims to present the discrepancy in oil film distribution in reciprocating motion experimentally with zero entraining velocity (ZEV) on a conventional ball-disk test rig with oil lubrication.

Design/methodology/approach

Driven independently by two individual servomotors, a steel ball and a sapphire disc move at equal speed but in opposite directions in a triangle wave. The oil film images between the ball and the disc were recorded by a camera. After the experiments, the mid-section film thickness was evaluated by using a dichromatic interference intensity modulation approach.

Findings

The dimpled oil film in transient condition is shallower than that at steady state with the same load and velocities, and the transient dimple depth decreases with the decrease of time. The increase of the applied load offers a beneficial effect on lubrication. Boundary slippage happens in ZEV reciprocating motion. The slippage at the interface is related to the transient effect and applied load.

Originality/value

This study reveals the significant difference of the oil film variation in ZEV reciprocating motion, especially the complex boundary slippage at the interface of the oil and the sapphire disc.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-01-2020-0021
Motivation and sustained participation in the online crowdsourcing community: the moderating role of community commitment
Authors: Wu Wei , Gong Xiang
Published: September 2020

Purpose

Crowdworkers' sustained participation is critical to the success and sustainability of the online crowdsourcing community. However, this issue has not received adequate attention in the information systems research community. This study seeks to understand the formation of crowdworker sustained participation in the online crowdsourcing community.

Design/methodology/approach

The research model was empirically tested using online survey data from 212 crowdworkers in a leading online crowdsourcing community in China.

Findings

The empirical results provide several key findings. First, there are two different types of sustained participation: continuous participation intention (CPI) and increased participation intention (IPI). Second, extrinsic motivation and intrinsic motivation positively influence crowdworker CPI and IPI. Third, community commitment negatively moderates the effects of extrinsic motivation on CPI and IPI, while it positively moderates the effects of intrinsic motivation on CPI and IPI.

Originality/value

This study has significant implications for research on online crowdsourcing community and provides practical guidance for formulating persuasive measures to promote crowdworker sustained participation in the community.
The impact of equity incentive plans (EIPs) on accounting conservatism in listed Chinese firms
Authors: Liu Sun , Zhang Jie
Published: September 2020

Purpose

This study investigates whether listed firms using equity incentive plans (EIPs) adopt more conservative accounting in China's unique corporate setting.

Design/methodology/approach

Based on a sample of 2,243 listed firms and 9,950 firm-year observations for the period of 2008–2017, this study employs piecewise cross-sectional regression models with year and industry fixed effects to examine the associations proposed in the research hypotheses.

Findings

This study finds a positive relationship between the adoption of EIPs and accounting conservatism in listed Chinese firms. Further analyses reveal that this positive relationship is more pronounced when listed Chinese firms use restricted stock units (RSUs), instead of stock options, in their EIPs.

Research limitations/implications

Unlike many early studies, this paper empirically investigates the impacts of two different types of equity incentives – stock options and RSUs – and thus contributes to accounting and corporate governance literature by providing a better understanding of the impacts of different types of equity incentives on financial reporting quality. However, this study does not consider other alternative equity incentive measurements because of the limited data regarding Chinese firm's executive compensation.

Practical implications

This study offers investors and policymakers in China some insight into how accounting conservatism in listed firms might be shaped by equity incentives used in their managerial compensation schemes.

Originality/value

This study is one of the few that examines the effects of using equity incentives in a large emerging market. It offers support for the view that the recent introduction of policies on EIPs by the Chinese government has an overall positive impact on listed firm's financial reporting quality, as reflected by greater degrees of accounting conservatism.
Social media as a tool of knowledge sharing in academia: an empirical study using valance, instrumentality and expectancy (VIE) approach
Authors: Chatterjee Sheshadri , Rana Nripendra P. , Dwivedi Yogesh K.
Published: September 2020

Purpose

The purpose of this paper is to understand the factors that determine the knowledge exchange intention and behavioural nature of academics by the help of social media tools in the Indian higher education.

Design/methodology/approach

This study has used valance–instrumentality–expectancy (VIE) theory to determine the knowledge exchange behaviour of academics. The study has considered the effects of knowledge contributor (KC) and knowledge seeker (KS) as moderators. The model has been validated by using a survey with 320 usable respondents.

Findings

The results highlight that if the stakeholders of higher education institutions feel the deficits of knowledge exchange, they realize importance of knowledge sharing and use social media to increase effect of knowledge exchange. Besides, perceived usefulness impacts on the use of social media for knowledge exchange by the concerned stakeholders. Moreover, it is observed that experience of the use of social media impacts the use of this tool for knowledge exchange.

Research limitations/implications

The use and application of VIE theory have successfully been able to interpret the factors affecting use of social media for knowledge exchange in higher educational institutes. The use of VIE theory has also been able to explain the proposed model better as the model could achieve a high explanative power (87%).

Practical implications

This study has provided meaningful insights to the practitioners and policymakers to realize how the stakeholders of the higher education institutions in India can be motivated to feel the need of sharing of knowledge and how they can use social media with ease for this purpose.

Originality/value

Not much research has been conducted with regard to the usage of social media as a tool for knowledge sharing in higher education sector in India. In that sense, this study is a novel attempt to undertake such research.