bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated Bile Acid Profile Analysis for The Non-invasive Staging Diagnosis of Ulcerative Colitis
Authors: Cao Lijuan , Wang Yun , Zhang Lu , Che Yuan , Huang Hai , Shen Hong , Hao Haiping
Published: March 2022

Clinical staging diagnosis and progression tracking for ulcerative colitis (UC) is challenging as poor patient compliance of endoscopic biopsy, we aimed to explore a non-invasive integrative biochemical index to quantitative track and monitor pathological activity. Here we perform a study that integrates bile acid metabolomic profiling, metagenomic sequencing and clinical monitoring on serum and feacal samples from 24 active-state UC patients, 25 remission-state UC patients and 20 healthy volunteers from China. Besides known associations of Fusobacterium nucleatum and Peptostreptococcus stomatis with UC, we found several bile acid-transforming species, including 7α-dehydroxygenase and 7α/β-dehydrogenase expressing microbiota, were significant correlated with UC pathological activity. We identified 7 microbial gene markers that differentiated active and remission-stage UC and healthy control microbiomes. Relevantly, decreased serum deoxycholic acid /cholic acid ratio and increased fecal ursodeoxycholic acid/chenodeoxycholic acid ratio were associated with pathological activity of UC. Moreover, receiver operating characteristic analysis based on serum/fecal bile acids ratios was much accurate in prediction of active and remission stage outcome. This species-specific temporal change and bile acid dysregulation pattern linked to disease severity indicating that integrated microbiome-bile acid profile maybe implied for disease activity prediction, and that targeting microbiome-mediated restoring gut flora and bile acids homeostasis may be implicative of therapy efficacy. Collectively, these insights will help improve clinical diagnosis and optimize existing medical treatments.
Exogenous application of dsRNA for the control of viruses in cucurbits
Authors: Delgado-Martín Josemaría , Ruiz Leticia , Janssen Dirk , Velasco Leonardo
Published: March 2022

The recurrent emergence of virus diseases in intensive horticultural crops requires alternative control strategies. Topical application of dsRNA molecules homologous to pathogens has been proposed as a tool for plant virus control. These dsRNAs induce the silencing mechanism (RNAi) that degrades homologous dsRNAs. Cucumber green mottle mosaic virus (CGMMV) represents a serious threat to cucurbit crops. Since genetic resistance to the virus is not yet available in commercial varieties, we aimed to control this virus by RNAi. For this purpose, we obtained constructions both for expressing dsRNA in bacteria to treat cucumber plants by topical application and for agroinoculation in experiments done in the growth chamber. Besides, greenhouse tests were performed in spring and in summer when plants were challenged with the virus and differences in several parameters were investigated, including severity of symptoms, dry weight, total height, virus accumulation and virus-derived small interfering RNAs (vsiRNAs). Spraying of plants with dsRNA reduced significatively CGMMV symptoms in the plants in growth chamber tests. Agroinfiltration experiments done under identical conditions were also effective in limiting the progress of CGMMV disease. In the greenhouse assay performed in spring, symptoms were significatively reduced in dsRNA-sprayed plants and the development of the plants improved with respect to non-treated plants. Virus titters and vsiRNAs were clearly reduced in dsRNA-treated plants. The effect of protection of the dsRNA was less evident in the greenhouse assay carried out in summer. Besides, we investigated the mobility of long (ds)RNA derived from spraying or agroinfiltrated dsRNA and found that it could be detected in local, close distal and far distal points from the site of application. VsiRNAs were also detected in local and distal points and the differences in accumulation were compared. In parallel, we investigated the capacity of dsRNAs derived from genes of tomato leaf curl New Delhi virus (ToLCNDV), another economically important virus in cucurbits, to limit the disease in zucchini, both by agroinfiltration or direct spraying, but found no protection effect. In view of the results, topical application of dsRNAs is postulated as a promising strategy for CGMMV control in cucumber.
Human alveolar macrophage response toMycobacterium tuberculosis: immune characteristics underlying large inter-individual variability
Authors: Sadee Wolfgang , Cheeseman Ian H. , Papp Audrey , Pietrzak Maciej , Seweryn Michal , Zhou Xiaofei , Lin Shili , Williams Amanda M. , Arnett Eusondia , Azad Abul K. , Schlesinger Larry S.
Published: March 2022

Mycobacterium tuberculosis(M.tb) establishes residence and growth in human alveolar macrophages (AMs). Large inter-individual variation inM.tb-AM interactions is a potential early indicator of TB risk and efficacy of therapies and vaccines. Herein, we systematically analyze interactions of a virulentM.tbstrain with freshly isolated human AMs from 28 healthy adult donors, measuring host RNA expression and secreted candidate proteins associated with TB pathogenesis over 72h. We observe large inter-individual differences in bacterial uptake and growth, with tenfold variation inM.tbload at 72h, reflected by large variation of gene expression programs. Systems analysis of differential and variable RNA and protein expression identifies TB-associated genes and networks (e.g., IL1BandIDO1). RNA time profiles document early stimulation of M1-type macrophage gene expression followed by emergence of an M2-type profile. The fine-scale resolution of this work enables the separation of genes and networks regulating earlyM.tbgrowth dynamics, and development of potential markers of individual susceptibility toM.tbinfection and response to therapies.
Claudin5 protects the peripheral endothelial barrier in an organ and vessel type-specific manner
Authors: Richards M , Nwadozi E , Pal S , Martinsson P , Kaakinen M , Gloger M , Sjöberg E , Koltowska K , Betsholtz C , Eklund L , Nordling S , Claesson-Welsh L
Published: March 2022

The pathogenesis of numerous diseases is characterised by disruption of the junctions that form the endothelial cell (EC) barrier, the composition of which may differ greatly between organs. However, the expression level variability and precise contribution of different junctional proteins is poorly understood. Here, we focus on organs with continuous endothelium to identify structural and functional in vivo characteristics of the EC barrier. Assembly of multiple single-cell RNAseq datasets into a single integrated database revealed the variability in EC barrier patterning. Across tissues Claudin5 exhibited diminishing expression along the arteriovenous axis, which correlates with EC barrier integrity. Functional analysis identified tissue-specific differences in leakage patterning and response to agonist-induced leakage. We uncover that Claudin5 loss enhances agonist-induced leakage in an organotypic, vessel type-specific and size-selective manner in an inducible, EC-specific, knock-out mouse. Mechanistically, Claudin5 loss induces no change in junction ultrastructure but alters composition, with concomitant loss of zonula occludens-1 (ZO-1) expression and upregulation of VE-Cadherin. These findings uncover the organ-specific organisation of the EC barrier and distinct importance of Claudin5 in different vascular beds and will aid our ability to modify EC barrier stability in a targeted, organ-specific manner.
Reciprocal feature encoding by cortical excitatory and inhibitory neurons
Authors: Duszkiewicz Adrian J. , Orhan Pierre , Skromne Carrasco Sofia , Brown Eleanor H. , Owczarek Eliott , Vite Gilberto R. , Wood Emma R. , Peyrache Adrien
Published: March 2022

In the cortex, the interplay between excitation and inhibition determines the fidelity of neuronal representations. However, while the receptive fields of excitatory neurons are often fine-tuned to the encoded features, the principles governing the tuning of inhibitory neurons are still elusive. We addressed this problem by recording populations of neurons in the postsubiculum (PoSub), a cortical area where the receptive fields of most excitatory neurons correspond to a specific head-direction (HD). In contrast to PoSub-HD cells, the tuning of fast-spiking (FS) cells, the largest class of cortical inhibitory neurons, was broad and heterogeneous. However, we found that PoSub-FS cell tuning curves were often fine-tuned in the spatial frequency domain, which resulted in various radial symmetries in their HD tuning. In addition, recordings and specific optogenetic manipulations of the upstream thalamic populations as well as computational models suggest that this population co-tuning in the frequency domain has a local origin. Together, these findings provide evidence that the resolution of neuronal tuning is an intrinsic property of local cortical networks, shared by both excitatory and inhibitory cell populations.
Neutralizing responses in fully vaccinated with BNT162b2, CoronaVac, ChAdOx1, and Ad26.COV2.S against SARS-CoV-2 lineages in Colombia, 2020-2021
Authors: Álvarez-Díaz Diego A. , Muñoz Ana Luisa , Herrera-Sepúlveda María T. , Tavera-Rodríguez Pilar , Laiton-Donato Katherine , Franco-Muñoz Carlos , Ruiz-Moreno Héctor Alejandro , Pelaez-Carvajal Dioselina , Muñoz-Suarez Alejandra M. , Galindo Marisol , Reales-Gonzalez Jhonnatan , Catama Jenssy D. , De Arco Beatriz Helena , Cobos Tatiana , Arias-Ramirez Edgar J. , Mercado-Reyes Marcela
Published: March 2022

Background

By March 2022, around 34 million people in Colombia had received a complete scheme of vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including, mRNA-based vaccines, viral vectored coronavirus vaccines, or the inactivated whole virus vaccine. However, as several SARS-CoV-2 variants of concern (VOC) and interest (VOI) co-circulate in the country, determining the resistance level to vaccine-elicited neutralizing antibodies (nAbs) is useful to improve the efficacy of COVID-19 vaccination programs.

Methods

Microneutralization assays with the most prevalent SARS-CoV-2 lineages in Colombia during 2020-2021 were performed using serum samples from immunologically naïve individuals between 9 and 13 weeks after receiving complete regimens of CoronaVac, BNT162b2, ChAdOx1, or Ad26.COV2.S. The mean neutralization titer (MN50) was calculated by the Reed–Muench method and used to determine differences in vaccine-elicited nAbs against the SARS-CoV-2 lineages B.1.111, P.1 (Gamma), B.1.621 (Mu), and AY.25.1 (Delta).

Results

The most administered vaccines in the country, BNT162b2 and CoronaVac, elicited significantly different nAb responses against Mu, as the GMTs were 75.7 and 5.9-fold lower relative to the control lineage (B.1.111), while for Delta were 15.8 and 1.1-fold lower, respectively. In contrast, nAb responses against Mu and Delta were comparable between ChAd0×1-s and Ad26.COV2.S as the GMTs remained around 5 to 7-fold lower relative to B.1.111.

Conclusions

The emergence of SARS-CoV-2 variants in Colombia with a significant capacity to escape from vaccine-elicited nAbs indicates that a booster dose is highly recommended. Furthermore, other non-pharmacological measures should be retained in the vaccinated population.
Deep kinetoplast genome analyses result in a novel molecular assay for detecting Trypanosoma brucei gambiense-specific minicircles
Authors: Geerts Manon , Chen Zihao , Bebronne Nicolas , Savill Nicholas J. , Schnaufer Achim , Büscher Philippe , Van Reet Nick , Van den Broeck Frederik
Published: March 2022

The World Health Organization targeted Trypanosoma brucei gambiense (Tbg) human African trypanosomiasis for elimination of transmission by 2030. Sensitive molecular markers that specifically detect Tbg type 1 (Tbg1) parasites will be important tools to assist in reaching this goal. Here, we aim at improving molecular diagnosis of Tbg1 infections by targeting the abundant mitochondrial minicircles within the kinetoplast of Trypanosoma brucei parasites. Using Next-Generation Sequencing of total cellular DNA extracts, we assembled and annotated the kinetoplast genome and investigated minicircle sequence diversity in 38 animal- and human-infective trypanosome strains. Computational analyses recognized a total of 241 Minicircle Sequence Classes as Tbg1-specific, of which three were shared by the 18 studied Tbg1 strains. We then developed a novel multiplex quantitative PCR assay (g-qPCR3) targeting one Tbg1-specific minicircle and three Tbg1-specific or Trypanozoon-specific markers. Molecular analyses revealed that the minicircle-based assay is applicable on animals and is as specific as the TgsGP-based assay, the current golden standard for molecular detection of Tbg1. The median copy number of the targeted minicircle was equal to eight, suggesting that our minicircle-based assay may be used for the sensitive detection of Tbg1 parasites. Finally, annotation of the targeted minicircle sequence indicated that it encodes genes essential for the survival of the parasite, and will thus likely be preserved in natural Tbg1 populations. These results demonstrated that our minicircle-based assay is a promising new tool for reliable and sensitive detection of Tbg1 infections in humans and animals.
SARS-CoV-2 infection during the Omicron surge among patients receiving dialysis: the role of circulating receptor-binding domain antibodies and vaccine doses
Authors: Montez-Rath Maria E. , Garcia Pablo , Han Jialin , Cadden LinaCel , Hunsader Patti , Morgan Curt , Kerschmann Russell , Beyer Paul , Dittrich Mary , Block Geoffrey A , Anand Shuchi , Parsonnet Julie , Chertow Glenn M
Published: March 2022

Background

It is unclear whether a third dose of mRNA platform vaccines, or antibody response to prior infection or vaccination confer protection from the Omicron variant among patients receiving dialysis.

Methods

Monthly since February 2021, we tested plasma from 4,697 patients receiving dialysis for antibodies to the receptor-binding domain (RBD) of SARS-CoV-2. We assessed semiquantitative median IgG index values over time among patients vaccinated with at least one dose of the two mRNA vaccines. We ascertained documented COVID-19 diagnoses after December 25, 2021 and up to January 31, 2022. We estimated the relative risk for documented SARS-CoV-2 infection by vaccination status using a log-binomial model accounting for age, sex, and prior clinical COVID-19. Among patients with RBD IgG index value available during December 1-December 24, 2021, we also evaluated the association between the circulating RBD IgG titer and risk for Omicron variant SARS-CoV-2 infection.

Results

Of the 4,697 patients we followed with monthly RBD assays, 3576 are included in the main analysis cohort; among these, 852 (24%) were unvaccinated. Antibody response to third doses was robust (median peak index IgG value at assay limit of 150, equivalent to 3270 binding antibody units/mL). Between December 25-January 31, 2022, SARS-CoV-2 infection was documented 340 patients (7%), 115 (36%) of whom were hospitalized. The final doses of vaccines were given a median of 272 (25th, 75thpercentile, 245-303) days and 58 (25th, 75thpercentile, 51-95) days prior to infection for the 1-2 dose and 3 dose vaccine groups respectively. Relative risks for infection were higher among patients without vaccination (RR 2.1 [95%CI 1.6, 2.8]), and patients with 1-2 doses (RR 1.3 [95%CI 1.0, 1.8]), compared with patients with three doses of the mRNA vaccines. Relative risks for infection were higher among patients with RBD index values < 23 (506 BAU/mL), compared with RBD index value ≥ 23 (RR 2.4 [95%CI 1.9, 3.0]). The higher risk for infection among patients with RBD index values < 23 was present among patients who received three doses (RR 2.1 [95%CI 1.3, 3.4]).

Conclusions

Among patients receiving hemodialysis, patients unvaccinated, without a third mRNA vaccine dose, or those lacking robust circulating antibody response are at higher risk for Omicron variant infection. Low circulating antibodies could identify the subgroup needing intensified surveillance, prophylaxis or treatment in this patient population.
Molecular Crowding Facilitates Bundling of IMPDH Polymers and Cytoophidium Formation
Authors: Chang Chia-Chun , Peng Min , Zhong Jiale , Zhang Ziheng , Keppeke Gerson Dierley , Sung Li-Ying , Liu Ji-Long
Published: March 2022

The cytoophidium is a unique type of membraneless compartment comprising of filamentous protein polymers. Inosine monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step of de novo GTP biosynthesis and plays critical roles in active cell metabolism. However, the molecular regulation of cytoophidium formation is poorly understood. Here we show that human IMPDH2 polymers bundle up to form cytoophidium-like aggregates in vitro when macromolecular crowders are present. The self-association of IMPDH polymers is suggested to rely on electrostatic interactions. In cells, the increase of molecular crowding with hyperosmotic medium induces cytoophidia, while the decrease of that by the inhibition of RNA synthesis perturbs cytoophidium assembly. In addition to IMPDH, CTPS and PRPS cytoophidium could be also induced by hyperosmolality, suggesting a universal phenomenon of cytoophidium-forming proteins. Finally, our results indicate that the cytoophidium can prolong the half-life of IMPDH, which is proposed to be one of conserved functions of this subcellular compartment.
Epilepsy-related CDKL5 deficiency slows synaptic vesicle endocytosis in central nerve terminals
Authors: Kontaxi Christiana , Davenport Elizabeth C. , Kind Peter C. , Cousin Michael A.
Published: March 2022

Cyclin-dependent kinase-like 5 (CDKL5) deficiency disorder (CDD) is a severe early-onset epileptic encephalopathy resulting mainly from de novo mutations in the X-linked CDKL5 gene. To determine whether loss of presynaptic CDKL5 function contributes to CDD, we examined synaptic vesicle (SV) recycling in primary hippocampal neurons generated from a Cdkl5 knockout rat model. Using a genetically-encoded reporter, we revealed that CDKL5 is selectively required for efficient SV endocytosis. We showed that CDKL5 kinase activity is both necessary and sufficient for optimal SV endocytosis, since kinase-inactive mutations failed to correct endocytosis in Cdkl5 knockout neurons, whereas the isolated CDKL5 kinase domain fully restored SV endocytosis kinetics. Finally, we demonstrated that CDKL5-mediated phosphorylation of amphiphysin 1, a putative presynaptic target, is not required for CDKL5-dependent control of SV endocytosis. Overall, our findings reveal a key presynaptic role for CDKL5 kinase activity and enhance our insight into how its dysfunction may culminate in CDD.
Cell size and actin architecture determine force generation in optogenetically activated adherent cells
Authors: Andersen T , Wörthmüller D , Probst D , Wang I , Moreau P , Fitzpatrick V , Boudou T , Schwarz US , Balland M
Published: March 2022

Adherent cells use actomyosin contractility to generate mechanical force and to sense the physical properties of their environment, with dramatic consequences for migration, division, differentiation and fate. However, the organization of the actomyosin system within cells is highly variable, with its assembly and function being controlled by small GTPases from the Rho-family. How activation of these regulators translates into cell-scale force generation and the corresponding sensing capabilities in the context of different physical environments is not understood. Here we probe this relationship combining recent advances in non-neuronal optogenetics with micropatterning and traction force microscopy on soft elastic substrates. We find that after whole-cell RhoA-activation by the CRY2/CIBN optogenetic system with a short pulse of 100 milliseconds, single cells contract before returning to their original tension setpoint with near perfect precision on a time scale of several minutes. To decouple the biochemical and mechanical elements of this response, we introduce a mathematical model that is parametrized by fits to the dynamics of the substrate deformation energy. We find that the RhoA-response builds up quickly on a time scale of 20 seconds, but decays slowly on a time scale of 50 seconds. The larger the cells and the more polarized their actin cytoskeleton, the more substrate deformation energy is generated. RhoA-activation starts to saturate if optogenetic pulse length exceeds 50 milliseconds, revealing the intrinsic limits of biochemical activation. Together our results suggest that adherent cells establish tensional homeostasis by the RhoA-system, but that the setpoint and the dynamics around it are strongly determined by cell size and the architecture of the actin cytoskeleton, which both are controlled by the extracellular environment.
Broad-spectrum extracellular antiviral properties of Cucurbit[n]urils
Authors: Jones Luke M. , Super Elana H. , Batt Lauren J. , Gasbarri Matteo , Cheesman Benjamin T. , Howe Andrew M. , Coulston Roger , Jones Samuel T.
Published: March 2022

Viruses are microscopic pathogens capable of causing disease and are responsible for a range of human mortality and morbidity worldwide. They can be rendered harmless or destroyed with a range of antiviral chemical compounds. Cucurbit[n]urils (CB[n]s) are a macrocycle chemical compound existing as a range of homologues; due to their structure they can bind to biological materials, acting as supramolecular “hosts” to “guests”, such as amino acids. Due to the increasing need for a non-toxic antiviral compound, we investigated whether cucurbit[n]urils could act in an antiviral manner. We have found that certain cucurbit[n]uril homologues do indeed have an antiviral effect against a range of viruses, including RSV and SARS-CoV-2. In particular, we demonstrate that CB[7] is the active homologue of CB[n] mixtures, having an antiviral effect against enveloped and non-enveloped species. High levels of efficacy were observed with five-minute contact times across different viruses. We also demonstrate that CB[7] acts with an extracellular virucidal mode of action via host-guest supramolecular interactions between viral surface proteins and the CB[n] cavity, rather than via cell internalisation or a virustatic mechanism. This finding demonstrates that CB[7] acts as a supramolecular virucidal antiviral (a mechanism distinct from other current extracellular antivirals) demonstrating the potential of supramolecular interactions for future antiviral disinfectants.
Self-association features of NS1 proteins from different flaviviruses
Authors: Poveda-Cuevas Sergio A. , Etchebest Catherine , da Silva Fernando L. Barroso
Published: March 2022

Flaviviruses comprise a large group of arboviral species that are distributed in several countries of the tropics, neotropics, and some temperate zones. Since they can produce neurological pathologies or vascular damage, there has been intense research seeking better diagnosis and treatments for their infections in the last decades. The flavivirus NS1 protein is a relevant clinical target because it is involved in viral replication, immune evasion, and virulence. Being a key factor in endothelial and tissue-specific modulation, NS1 has been largely studied to understand the molecular mechanisms exploited by the virus to reprogram host cells. A central part of the viral maturation processes is the NS1 oligomerization because many stages rely on these protein-protein assemblies. In the present study, the self-associations of NS1 proteins from Zika, Dengue, and West Nile viruses are examined through constant-pH coarse-grained biophysical simulations. Free energies of interactions were estimated for different oligomeric states and pH conditions. Our results show that these proteins can form both dimers and tetramers under conditions near physiological pH even without the presence of lipids. Moreover, pH plays an important role mainly controlling the regimes where van der Waals interactions govern their association. Finally, despite the similarity at the sequence level, we found that each flavivirus has a well-characteristic protein-protein interaction profile. These specific features can provide new hints for the development of binders both for better diagnostic tools and the formulation of new therapeutic drugs.

Abstract Figure
The X chromosome is a potential polarising signal for asymmetric cell divisions in meiotic cells of a nematode
Authors: Alyazeedi Talal , Xu Emily , Kaur Jasmin , Shakes Diane , Pires-daSilva Andre
Published: March 2022

The unequal partition of molecules and organelles during cell division results in daughter cells with different fates. Asymmetric cell divisions have been best characterised in systems in which extrinsic signals polarise the mother cell during cell division. However, the mechanisms of asymmetric cell division mediated by intrinsic signals, and the nature of these signals, are mostly unknown. Here we report an asymmetric cell division in the nematode Auanema rhodensis that may be cued by the X chromosome. In the wildtype XO male, the spermatocyte divides asymmetrically to generate X-bearing spermatids that inherit components necessary for sperm viability, and nullo-spermatids that inherits components to be discarded. We found that in XX mutant pseudomales, sperm components co-segregate with the X chromosome, supporting the hypothesis that the X chromosome is employed as a polarising signal for partitioning essential cytoplasmic components for sperm function.
QTLViewer: An interactive webtool for genetic analysis in the Collaborative Cross and Diversity Outbred mouse populations
Authors: Vincent Matthew , Gyuricza Isabela Gerdes , Keele Gregory R , Gatti Daniel M , Keller Mark P , Broman Karl W , Churchill Gary A
Published: March 2022

The Collaborative Cross (CC) and the Diversity Outbred (DO) mouse populations are related multiparental populations (MPPs), derived from the same eight isogenic founder strains. They carry >50M known genetic variants, which makes them ideal tools for mapping genetic loci that regulate phenotypes, including physiological and molecular traits. Mapping quantitative trait loci (QTLs) requires statistical and computational training, which can present a barrier to access for some researchers. The QTLViewer software is graphical user interface webtool for CC and DO studies that performs QTL mapping through the R/qtl2 package. Additionally, the QTLViewer website serves as a repository for published CC and DO studies, allowing users to explore QTL mapping results interactively and increasing the accessibility of these genetic resources to the broader scientific community.
A large and rich EEG dataset for modeling human visual object recognition
Authors: Gifford Alessandro T. , Dwivedi Kshitij , Roig Gemma , Cichy Radoslaw M.
Published: March 2022

The human brain achieves visual object recognition through multiple stages of nonlinear transformations operating at a millisecond scale. To predict and explain these rapid transformations, computational neuroscientists employ machine learning modeling techniques. However, state-of-the-art models require massive amounts of data to properly train, and to the present day there is a lack of vast brain datasets which extensively sample the temporal dynamics of visual object recognition. Here we collected a large and rich dataset of high temporal resolution EEG responses to images of objects on a natural background. This dataset includes 10 participants, each with 82,160 trials spanning 16,740 image conditions. Through computational modeling we established the quality of this dataset in five ways. First, we trained linearizing encoding models that successfully synthesized the EEG responses to arbitrary images. Second, we correctly identified the recorded EEG data image conditions in a zero-shot fashion, using EEG synthesized responses to hundreds of thousands of candidate image conditions. Third, we show that both the high number of conditions as well as the trial repetitions of the EEG dataset contribute to the trained models’ prediction accuracy. Fourth, we built encoding models whose predictions well generalize to novel participants. Fifth, we demonstrate full end-to-end training of randomly initialized DNNs that output M/EEG responses for arbitrary input images. We release this dataset as a tool to foster research in visual neuroscience and computer vision.
Sensorimotor transformation underlying odor-modulated locomotion in walking Drosophila
Authors: Tao Liangyu , Wechsler Samuel P , Bhandawat Vikas
Published: March 2022

Most real-world behaviors are performed with incomplete information. Odor-guided locomotion, an ecologically important behavior essential to an animal’s survival, is an example of such a behavior. Different odors activate different patterns of olfactory receptor neuron (ORN) classes providing information about which odor is present but does not provide any navigational information. In this study, we investigate the sensorimotor transformation that relates ORN activation to locomotion changes in Drosophila by optogenetically activating different combinations of ORN classes and measuring the resulting changes in locomotion. Three features describe this sensorimotor transformation: First, locomotion depends on both the instantaneous firing frequency (f) and its change (df); the two together serve as short-term memory that allows the fly to automatically adapt its motor program to sensory context. Second, the mapping between f-df and locomotor parameters such as speed or curvature is distinct for each pattern of activated ORNs. Finally, the sensorimotor mapping changes with time after odor exposure allowing integration of information over a longer timescale.
Replication-dependent organisation constrains positioning of long DNA repeats in bacterial genomes
Authors: Malhotra Nitish , Seshasayee Aswin Sai Narain
Published: March 2022

Bacterial genome organisation is primarily driven by chromosome replication from a single origin of replication. However chromosomal rearrangements, which can disrupt such organisation, are inevitable in nature. Long DNA repeats are major players mediating rearrangements, large and small, via homologous recombination. Since changes to genome organisation affect bacterial fitness - and more so in fast-growing than slow-growing bacteria - and are under selection, it is reasonable to expect that genomic positioning of long DNA repeats is also under selection. To test this, we identified identical DNA repeats of at least 100 base pairs across ~6,000 bacterial genomes and compared their distribution in fast and slow growing bacteria. We find that long identical DNA repeats are distributed in a non-random manner across bacterial genomes. Their distribution differs in their overall number, orientation and proximity to the origin of replication, in fast and slow growing bacteria. We show that their positioning - which might arise from a combination of the processes that produce repeats and selection on rearrangements that recombination between repeat elements might cause - permits minimum disruption to the replication-dependent genome organisation of bacteria, thus acting as a major constraint.
On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy
Authors: Sorzano C. O. S. , Jiménez-Moreno A. , Maluenda D. , Martínez M. , Ramírez-Aportela E. , Krieger J. , Melero R. , Cuervo A. , Conesa J. , Filipovic J. , Conesa P. , del Caño L. , Fonseca Y. C. , Jiménez-de la Morena J. , Losana P. , Sánchez-García R. , Strelak D. , Fernández-Giménez E. , de Isidro-Gómez F. P. , Herreros D. , Vilas J. L. , Marabini R. , Carazo J. M.
Published: March 2022

Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands of macromolecules that are assumed to be structurally identical are combined into a single 3D map representing the Coulomb potential of the macromolecule under study. This article discusses possible caveats along the image-processing path and how to avoid them to obtain a reliable 3D structure. Some of these problems are very well known in the community. These may be referred to as sample-related (such as specimen denaturation at interfaces or non-uniform projection geometry leading to underrepresented projection directions). The rest are related to the algorithms used. While some have been discussed in depth in the literature, such as the use of an incorrect initial volume, others have received much less attention. However, they are fundamental in any data-analysis approach. Chiefly among them, instabilities in estimating many of the key parameters that are required for a correct 3D reconstruction that occur all along the processing workflow are referred to, which may significantly affect the reliability of the whole process. In the field, the term overfitting has been coined to refer to some particular kinds of artifacts. It is argued that overfitting is a statistical bias in key parameter-estimation steps in the 3D reconstruction process, including intrinsic algorithmic bias. It is also shown that common tools (Fourier shell correlation) and strategies (gold standard) that are normally used to detect or prevent overfitting do not fully protect against it. Alternatively, it is proposed that detecting the bias that leads to overfitting is much easier when addressed at the level of parameter estimation, rather than detecting it once the particle images have been combined into a 3D map. Comparing the results from multiple algorithms (or at least, independent executions of the same algorithm) can detect parameter bias. These multiple executions could then be averaged to give a lower variance estimate of the underlying parameters.
Industrial process data visualization based on a deep enhanced t-distributed stochastic neighbor embedding neural network
Authors: Lu Weipeng , Yan Xuefeng
Published: March 2022

Purpose

The purpose of this paper is to propose a approach for data visualization and industrial process monitoring.

Design/methodology/approach

A deep enhanced t-distributed stochastic neighbor embedding (DESNE) neural network is proposed for data visualization and process monitoring. The DESNE is composed of two deep neural networks: stacked variant auto-encoder (SVAE) and a deep label-guided t-stochastic neighbor embedding (DLSNE) neural network. In the DESNE network, SVAE extracts informative features of the raw data set, and then DLSNE projects the extracted features to a two dimensional graph.

Findings

The proposed DESNE is verified on the Tennessee Eastman process and a real data set of blade icing of wind turbines. The results indicate that DESNE outperforms some visualization methods in process monitoring.

Originality/value

This paper has significant originality. A stacked variant auto-encoder is proposed for feature extraction. The stacked variant auto-encoder can improve the separation among classes. A deep label-guided t-SNE is proposed for visualization. A novel visualization-based process monitoring method is proposed.
Labour force participation and unemployment rate: does discouraged worker effect hypothesis or unemployment invariance hypothesis hold in Africa?
Authors: Raifu Isiaka Akande , Adeboje Oluwafemi Mathew
Published: March 2022

Purpose

The purpose of this study is to examine the existence of discouraged worker effect hypothesis and unemployment invariance hypothesis in Africa, including its five regional groups. Specifically, the study tests the existence of co-integration between different categories of labour force participation and unemployment rate, total male and female labour force participation and the unemployment rate for age brackets 15–24, 15–64 and 15+, respectively.

Design/methodology/approach

The study uses the data of 52 countries in Africa which cover the period from 1991 to 2018. Three co-integration estimation techniques namely, the Kao co-integration test, Pedroni co-integration test and Westerlund co-integration test are used to validate the existence of co-integration between the labour force participation and unemployment rate. The dynamic ordinary least square is further used to explore the impact of the unemployment rate on labour force participation, while the pooled ordinary least squares (POLS) that accounts for individual country and time effects is employed for robustness check.

Findings

Except for Southern Africa, it is found that the discouraged worker effect hypothesis holds in Africa and the rest of its regions. This suggests that there is a long-run relationship between labour force participation rate and unemployment rate irrespective of age group and gender classifications. To some extent, the authors discover the existence of cross-sectional dependence in the panel. There is also an inverse relationship between labour force participation and the unemployment rate. This implies that when the unemployment rate is high, labour force participation tends to decline. The results are, however, sensitive to the choice of estimation method.

Research limitations/implications

The study is limited to the examination of linear co-integration between labour force participation and the unemployment rate in Africa and its five regions. The future study can investigate the possibility of a nonlinear or an asymmetric relationship between labour for participation and the unemployment rate.

Social implications

Thus, a policy framework that would generate employment creation is greatly required in Africa.

Originality/value

To the best of the authors’ knowledge, this is a pioneer work that addresses the issue of co-integration between labour force participation and unemployment rate for Africa and its five regions taking into consideration gender and age brackets of labour force participation and unemployment.
Influence of perceived environmental knowledge and environmental concern on customers' green hotel visit intention: mediating role of green trust
Authors: Sultana Nafia , Amin Sanjida , Islam Azharul
Published: March 2022

Purpose

The purpose of this study is twofold. First, it aims to examine the influence of customers' green considerations in the form of perceived green knowledge and environmental concern on their intention to stay at green hotels; and secondly, to explain the mediating role of green trust among the considered variables.

Design/methodology/approach

The study investigates green hotel visit perceptions of 213 customers of hotel industry of Dhaka, Bangladesh using Partial Least Square method. Data was collected using a standard structured questionnaire.

Findings

The findings display a significant positive influence of perceived green knowledge and green trust on customers' green hotel visit intention. Moreover, green trust mediates the relationship of green visit intentions with customers' green knowledge and environmental concern.

Practical implications

The study demonstrates that environmental knowledge and green trust make customers choose green hotels. The findings of the current study may assist the hotel business administrators to understand the underlying factors for choosing green hotels and adopting green practices in their business operations accordingly.

Originality/value

To the best knowledge of the researchers, the study is first to measure the mediating impact of green trust on the influential factors of customers' green hotel visit intention in Bangladesh. The result reveals how considered variables interact with each other to influence green hotel choice decisions.
Ethnic restaurants’ outdoor signage: the effect of colour and name on consumers’ food perceptions and dining intentions
Authors: Song Hanqun , Yang Huijun
Published: March 2022

Purpose

Outdoor signage, a key aspect of store atmospherics which influence consumer perceptions and behaviour, is largely overlooked in research on restaurants. Studies show that food perceptions relate positively to restaurant choice, but how outdoor signage influences these perceptions is unclear. Hence, the study aims to investigate the effect of signage colour and restaurant name on consumers' attitudes and purchase intentions.

Design/methodology/approach

This study uses a two (signage colour: blue-white vs. red-yellow) by two (restaurant name: typical vs. atypical) experimental design to investigate the impact of two key elements of corporate visual identity – logo colour and corporate name – on consumers’ attitudes (perceptions of food tastiness and healthiness) and purchase intentions. Two-way analysis of covariance, confirmatory factor analysis and PROCESS are used for data analysis.

Findings

There is a main effect of signage colour on consumers’ perceptions of food healthiness and purchase intentions, and restaurant name significantly affects consumers’ purchase intentions. In addition, there is an interaction effect of signage colour and restaurant name on food healthiness and purchase intentions, and food tastiness and healthiness are associated with purchase intentions.

Practical implications

A key managerial insight emerging from this study is that restaurants’ outdoor signage may be manipulated by restaurateurs to enhance consumers’ perceptions of food healthiness and tastiness, as well purchase intentions.

Originality/value

This study adopts a new angle on corporate visual identity and links existing theories with research on restaurant atmospherics, to explore how brands employing national identity symbols leverages consumers’ prior knowledge to enhance the influence of outdoor signage on their food perceptions and purchase intentions.
Assessment of information literacy skills and knowledge-based competencies in using electronic resources among medical students
Authors: Ganesan Perumal , Gunasekaran Mangai
Published: March 2022

Purpose

This paper aims to focus on the information literacy skills and how the resources are being used by medical students of Mahatma Gandhi Medical College and Research Institute (MGMCRI), Pondicherry, India. The main aim is to determine the medical students use, purpose, search strategies and sources through which aware and literacy skills acquired. Further, this paper aims to bring out the problems faced.

Design/methodology/approach

A survey method was conducted through a structured questionnaire distributed among 120 medical students from first year to fourth year. Stratified random sampling was used for selection of students.

Findings

Findings of the study revealed that medical students largely used medical databases such as Bentham Sciences, ProQuest, PubMed and MedlinePlus. Further, the paper reveals that majority used health information for updating their knowledge and to acquire general information. The students’ information literacy level found minimal, which may be the reason majority of the students found difficulty in locating the desired materials followed by irrelevant information, inadequate e-resources and lack of awareness reported some extent.

Originality/value

The recommendations made based on the study are expected to be beneficial to the authorities and library administration of the surveyed institution to take appropriate measures for effective utilization of resources.
Examining the effect of group prototypes and divergent strength of identification on the effectiveness of identity appeals
Authors: McGowan Miriam , Hassan Louise May , Shiu Edward
Published: March 2022

Purpose

Past research argues that identity-linking messages must use established descriptors of the social group (i.e. prototypical identity appeals) to be effective. The authors show that less established descriptors (i.e. identity-linking messages low in prototypicality) can be optimal for an important customer segment, namely, for those that affectively identify with the social group. This is because of the distinct self-motives underlying the cognitive and affective social identity dimensions.

Design/methodology/approach

A pilot and two experimental studies were conducted, using gender and nationality as the target identities.

Findings

Consumers feel more hopeful and have higher purchase intention for products advertised using identity depictions that fit with their predominant (uncertainty-reduction or self-enhancement) self-motive. Consumers predominantly high in affective/cognitive social identity prefer identity-linking messages that are low/high in prototypicality. An abstract mindset reverses these effects by encouraging a similarity focus.

Research limitations/implications

Future work should identify potential boundary conditions of the findings. Further, all studies use ascribed social groups. Future work should explore whether consumers relate differently to different social group, such as achieved groups, non-human groups or aspirational groups.

Practical implications

Adverts using established descriptors of a brand’s target social group may no longer fit the brand’s positioning. Understanding when and when not to use less established group descriptors to market brands is important for practitioners.

Originality/value

To the best of the authors’ knowledge, this is the first research to explore the conditions under which priming consumers’ identity using less/more established (i.e. low/high in prototypicality) descriptors has a beneficial, or detrimental, effect on consumers’ purchase intention. In understanding these effects, the authors draw on consumers’ self-motives underlying cognitive and affective identification, a distinction not yet made in the identity-linking communications literature. The authors also explore the mediating role of hope – a central motivating emotion – in identity marketing.
User perceptions and use of authentication methods: insights from youth in Mexico and Bosnia and Herzegovina
Authors: Hadzidedic Suncica , Fajardo-Flores Silvia , Ramic-Brkic Belma
Published: March 2022

Purpose

This paper aims to address the user perspective about usability, security and use of five authentication schemes (text and graphical passwords, biometrics and hardware tokens) from a population not covered previously in the literature. Additionally, this paper explores the criteria users apply in creating their text passwords.

Design/methodology/approach

An online survey study was performed in spring 2019 with university students in Mexico and Bosnia and Herzegovina. A total of 197 responses were collected.

Findings

Fingerprint-based authentication was most frequently perceived as usable and secure. However, text passwords were the predominantly used method for unlocking computer devices. The participants preferred to apply personal criteria for creating text passwords, which, interestingly, coincided with the general password guidelines, e.g. length, combining letters and special characters.

Originality/value

Research on young adults’ perceptions of different authentication methods is driven by the increasing frequency and sophistication of security breaches, as well as their significant consequences. This study provided insight into the commonly used authentication methods among youth from two geographic locations, which have not been accounted for previously.