bluuebunny/crossref_metadata_2025 huggingface dataset:
Mouse models of NADK2 deficiency analyzed for metabolic and gene expression changes to elucidate pathophysiology
Authors: Murray G. , Bais P. , Hatton C. , Tadenev A.L.D. , Morelli K.H. , Schroeder D. , Doty R. , Fiehn O. , John S.W.M. , Bult C.J. , Cox G.A. , Burgess R.W.
Published: December 2021

NADK2 encodes the mitochondrial isoform of NAD Kinase, which phosphorylates nicotinamide adenine dinucleotide (NAD). Rare recessive mutations in human NADK2 are associated with a syndromic neurological mitochondrial disease that includes metabolic changes such as hyperlysinemia and 2,4 dienoyl CoA reductase (DECR) deficiency. However, the full pathophysiology resulting from NADK2 deficiency is not known. Here we describe two chemically-induced mouse mutations in Nadk2, S326L and S330P, which cause a severe neuromuscular disease and shorten lifespan. The S330P allele was characterized in detail and shown to have marked denervation of neuromuscular junctions by 5 weeks of age and muscle atrophy by 11 weeks of age. Cerebellar Purkinje cells also showed progressive degeneration in this model. Transcriptome profiling on brain and muscle was performed at early and late disease stages. In addition, metabolomic profiling was performed on brain, muscle, liver, and spinal cord at the same ages. Combined transcriptomic and metabolomic analyses identified hyperlysinemia, DECR deficiency, and generalized metabolic dysfunction in Nadk2 mutant mice, indicating relevance to the human disease. We compared findings from the Nadk model to equivalent RNAseq and metabolomic datasets from a mouse model of infantile neuroaxonal dystrophy, caused by recessive mutations in Pla2g6. This enabled us to identify disrupted biological processes that are common between these mouse models of neurological disease, such as translation, and those processes that are gene-specific such as glycolysis and acetylcholine binding. These findings improve our understanding of the pathophysiology of both Nadk2 and Pla2g6 mutations, as well as pathways common to neuromuscular/neurodegenerative diseases.
Phylogenomic analyses of Snodgrassella isolates from honeybees and bumblebees reveals taxonomic and functional diversity
Authors: Cornet Luc , Cleenwerck Ilse , Praet Jessy , Leonard Raphaël R. , Vereecken Nicolas J. , Michez Denis , Smagghe Guy , Baurain Denis , Vandamme Peter
Published: December 2021

Snodgrassella is a Betaproteobacteria genus found in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole genome sequences of 75 Snodgrassella strains from 4 species of honey bees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early on from the other species in their evolution, that isolates from honeybees and bumblebees were well separated and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees, i.e. Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species or group specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes.

Importance

The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee’s microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species, i.e. Snodgrassella alvi, has been named. Here we demonstrate that this genus is actually composed of at least seven species, two of them (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) being formally described in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.

Data summary

Cornet L and Vandamme P, European Nucleotide Archive (ENA), Project accession: PRJEB47378

Cornet L and Vandamme P, European Nucleotide Archive (ENA), Reads accessions: SAMEA9570070 - SAMEA9570078

Cornet L and Vandamme P, European Nucleotide Archive (ENA), Genome accessions: GCA_914768015, GCA_914768025, GCA_914768035, GCA_914768045, GCA_914768055, GCA_914768065, GCA_914768075, GCA_914768085, GCA_914768095.
Sequence diversity in the 3’ untranslated region of alphavirus modulates IFIT2-dependent restriction in a cell type-dependent manner
Authors: Hickson Sarah E. , Brekke Eden , Schwerk Johannes , Saluhke Indraneel , Zaver Shivam , Woodward Joshua , Savan Ram , Hyde Jennifer L.
Published: December 2021

Alphaviruses (family Togaviridae) are a diverse group of positive-sense RNA (+ssRNA) viruses that are transmitted by arthropods and are the causative agent of several significant human and veterinary diseases. Interferon (IFN)-induced proteins with tetratricopeptide repeats (IFITs) are a family of RNA-binding IFN stimulated genes (ISGs) that are highly upregulated following viral infection, and have been identified as potential restrictors of alphaviruses. The mechanism by which IFIT1 restricts RNA viruses is dependent on self and non-self-discrimination of RNA, and alphaviruses evade this recognition via their 5’UTR. However, the role of IFIT2 during alphavirus replication and the mechanism of viral replication inhibition is unclear. In this study, we identify IFIT2 as a restriction factor for Venezuelan equine encephalitis virus (VEEV) and show that IFIT2 binds the 3’ untranslated region (3’UTR) of the virus. We investigated the potential role of variability in the 3’UTR of the virus affecting IFIT2 antiviral activity by studying infection with VEEV. Comparison of recombinant VEEV clones containing 3’UTR sequences derived from epizootic and enzootic isolates exhibited differential sensitivity to IFIT2 restriction in vitro infection studies, suggesting that the alphavirus 3’UTR sequence may function in part to evade IFIT2 restriction. In vitro binding assays demonstrate that IFIT2 binds to the VEEV 3’UTR, however in contrast to previous studies VEEV restriction did not appear to be dependent on the ability of IFIT2 to inhibit translation of viral RNA, suggesting a novel mechanism of IFIT2 restriction. Our study demonstrates that IFIT2 is a restriction factor for alphaviruses and variability in the 3’UTR of VEEV can modulate viral restriction by IFIT2. Ongoing studies are exploring the biological consequences of IFIT2-VEEV RNA interaction in viral pathogenesis and defining sequence and structural features of RNAs that regulate IFIT2 recognition.
Age-specific Contribution of Contacts to Transmission of SARS-CoV-2 in Germany
Authors: Rodiah I. , Vanella P. , Kuhlmann A. , Jaeger V. K. , Harries M. , Krause G. , Bock W. , Lange B.
Published: December 2021

Introduction

Current estimates of pandemic spread using infectious disease models in Germany for SARS-CoV-2 often do not use age-specific infection parameters and are not always based on known contact matrices of the population. They also do not usually include setting-based information of reported cases and do not account for age-specific underdetection of reported cases. Here, we report likely pandemic spread using an age-structured model to understand the age- and setting-specific contribution of contacts to transmission during all phases of the COVID-19 pandemic in Germany.

Methods

We developed a deterministic SEIRS model using a pre-pandemic contact matrix. The model is optimized to fit reported age-specific SARS-CoV-2 incidences from the Robert Koch Institute, includes information on setting-specific reported cases in schools and integrates age and pandemic period-specific parameters for underdetection of reported cases deduced from a large population-based seroprevalence study.

Results

We showed that taking underreporting into account, younger adults and teenagers are the main contributors to infections during the first three pandemic waves in Germany. Overall, the contribution of contacts in schools to the total cases in the population was below 10% during the third wave.

Discussion

Accounting for the pandemic phase and age-specific underreporting seems important to correctly identify those parts of the population where quarantine, testing, vaccination, and contact-reduction measures are likely to be most effective and efficient. In the future, we will aim to compare current model estimates with currently emerging during-pandemic age-specific contact survey data.
Adult life-course trajectories of psychological distress and economic outcomes in midlife during the COVID-19 pandemic
Authors: Moulton V , Sullivan A , Goodman A , Parsons S , Ploubidis G
Published: December 2021

This study used two British birth cohorts to examine whether pre-pandemic trajectories of psychological distress were associated with a greater risk of changes in financial and employment situation during the pandemic, as well as increased need for government support and use of other methods to mitigate their economic situation. We identified 5 differential life-course trajectories of psychological distress from adolescence to midlife and explored their relation to changes in financial and employment circumstances at different stages during the pandemic from May 2020 to March 2021, applying multinomial logistic regression and controlling for numerous early life covariates. In addition, we ran modified Poisson models with robust standard errors to identify whether different trajectories were more likely to have been supported by the benefit system, payment holidays, borrowing and other methods of mitigating the economic shock. We found that despite the UK governments economic response package economic inequalities for pre-pandemic psychological distress trajectories with differential onset, severity and chronicity across the life-course were exacerbated by the COVID-19 economic shock. Furthermore, the subsequent cut in government support, alongside increases in the cost of living may widen economic inequalities for differential pre-pandemic psychological distress trajectories, which in turn may also worsen mental health. This work highlights, different pre-pandemic trajectories of psychological distress were more vulnerable to economic shock.
A spectrum of recessiveness among Mendelian disease variants in UK Biobank
Authors: Barton Alison R. , Hujoel Margaux L.A. , Mukamel Ronen E. , Sherman Maxwell A. , Loh Po-Ru
Published: December 2021

Recent work has found increasing evidence of mitigated, incompletely penetrant phenotypes in heterozygous carriers of recessive Mendelian disease variants. We leveraged whole-exome imputation within the full UK Biobank cohort (N∼500K) to extend such analyses to 3,481 rare variants curated from ClinVar and OMIM. Testing these variants for association with 57 quantitative traits yielded 103 significant associations involving variants previously implicated in 35 different diseases. Notable examples included a POR missense variant implicated in Antley-Bixler syndrome that associated with a 1.76 (s.e. 0.27) cm increase in height, and an ABCA3 missense variant implicated in interstitial lung disease that associated with reduced FEV1/FVC ratio. Association analyses with 1,257 disease traits yielded five additional variant-disease associations. We also observed contrasting levels of recessiveness between two more-common, classical Mendelian diseases. Carriers of cystic fibrosis variants exhibited increased risk of several mitigated disease phenotypes, whereas carriers of spinal muscular atrophy alleles showed no evidence of altered phenotypes. Incomplete penetrance of cystic fibrosis carrier phenotypes did not appear to be mediated by common allelic variation on the functional haplotype. Our results show that many disease-associated recessive variants can produce mitigated phenotypes in heterozygous carriers and motivate further work exploring penetrance mechanisms.
A Qualitative Expert Interview Study: Mobility Health in Indonesia
Authors: Yosia Mikhael , Basrowi Ray Wagiu , Sundjaya Tonny , Masita Bertri Maulidya
Published: December 2021

Background

Indonesia has an ageing population that can develop mobility health-related problems in the future, including osteoporosis, arthritis, sarcopenia, low back pain, neck pain, and peripheral neuropathy. However, there are limited references and research that look upon mobility health and problems surrounding it in Indonesia.

Aims

To improve understanding on issues surrounding mobility health in Indonesia through a semi-structured interview with relevant experts.

Method

Semi-structured qualitative interviews via phone calls were conducted with eight different experts. Data were analysed using reflexive thematic analysis. Experts with experience dealing with mobility (bone, muscle, joint, movement) related issues for more than ten years, working in Indonesia, and communicating in English or Bahasa Indonesia were included.

Results

Four themes were then identified across the experts on issues surrounding mobility health in Indonesia; this includes [1] screening and assessment of mobility health, [2] treatment for mobility health problems, [3] awareness campaign, [4] supplement for mobility health.

Conclusions

Diagnostic modalities for mobility health are abundant but still expensive. Treatment of mobility health with herbal medicine (jamu) might be beneficial. Fortified food or milk can improve mobility health. Social media can be a promising tool to increase awareness regarding mobility health. In general, there needs to be a change in mindset from curative to prevention in both health care providers and the general population.
learnMET: an R package to apply machine learning methods for genomic prediction using multi-environment trial data
Authors: Westhues Cathy C. , Simianer Henner , Beissinger Timothy M.
Published: December 2021

We introduce the R-package learnMET, developed as a flexible framework to enable a collection of analyses on multi-environment trial (MET) breeding data with machine learning-based models. learnMET allows the combination of genomic information with environmental data such as climate and/or soil characteristics. Notably, the package offers the possibility of incorporating weather data from field weather stations, or can retrieve global meteorological datasets from a NASA database. Daily weather data can be aggregated over specific periods of time based on naive (for instance, non-overlapping 10-day windows) or phenological approaches. Different machine learning methods for genomic prediction are implemented, including gradient boosted trees, random forests, stacked ensemble models, and multi-layer perceptrons. These prediction models can be evaluated via a collection of cross-validation schemes that mimic typical scenarios encountered by plant breeders working with MET experimental data in a user-friendly way. The package is fully open source and accessible on GitHub.
PTEN inhibits AMPK to control collective migration
Authors: Peglion Florent , Capuana Lavinia , Perfettini Isabelle , Braithwaite Ben , Quissac Emie , Forsberg-Nilsson Karin , Llense Flora , Etienne-Manneville Sandrine
Published: December 2021

PTEN is one of the most frequently mutated tumor suppressor gene in cancer. PTEN is generally altered in invasive cancers such as glioblastomas, but its function in collective cell migration and invasion is not fully characterized. Herein, we report that the loss of PTEN increases cell speed during collective migration of non-tumourous cells both in vitro and in vivo. We further show that loss of PTEN promotes LKB1-dependent phosphorylation and activation of the major metabolic regulator AMPK. In turn AMPK increases VASP phosphorylation, reduces VASP localization at cell-cell junctions and decreases the interjunctional transverse actin arcs at the leading front, provoking a weakening of cell-cell contacts and increasing migration speed. Targeting AMPK activity not only slows down PTEN-depleted cells, it also limits PTEN-null glioblastoma cell invasion, opening new opportunities to treat glioblastoma lethal invasiveness.
Endothelial-immune crosstalk contributes to vasculopathy in non-alcoholic fatty liver disease
Authors: Ng Chun Yi , Lee Khang Leng , Muthiah Mark D. , Wu Kan-Xing , Chioh Florence W. J. , Tan Konstanze , Soon Gwyneth S. T. , Shabbir Asim , Loo Wai Mun , Low Zun Siong , Chen Qingfeng , Tan Nguan Soon , Ng Huck Hui , Dan Yock Young , Cheung Christine
Published: December 2021

The top cause of mortality in patients with non-alcoholic fatty liver disease (NAFLD) is cardiovascular complications. However, the mechanisms of NAFLD-associated vasculopathy remain understudied. We developed blood outgrowth endothelial cell (BOEC) models from NAFLD and healthy subjects. NAFLD BOECs exhibited global transcriptional upregulation of chemokine hallmarks and human leukocyte antigens. In mouse models of diet-induced NAFLD, we further confirmed enhanced endothelial expressions of CXCL12 in the aortas and liver vasculatures. To elucidate endothelial-immune crosstalk, we performed immunoprofiling by single-cell analysis, uncovering T cell intensification and potentially T-helper type 1 inflammation in NAFLD patients. Functionally, interference of the CXCL12-CXCR4 axis by small molecule AMD3100 selectively modulated the chemotaxis of patient-derived CD4+ T cells and natural killer cells towards NAFLD BOECs, restoring endothelial barrier integrity. Clinically, we detected three folds more circulating damaged endothelial cells in NAFLD patients than healthy controls. Our work provides insights for modulation of interactions with effector immune subsets to mitigate endothelial injury in NAFLD.
The influence of Janthinobacterium sp. strain SLB01 on the cell culture of primmorphs of the sponge Lubomirskia baicalensis
Authors: Chernogor Lubov I. , Eliseikina Marina G. , Petrushin Ivan S. , Chernogor Ekaterina A. , Khanaev Igor V. , Belikov Sergei I.
Published: December 2021

Sponges (phylum Porifera) are ancient, filtering, multicellular metazoans. Freshwater sponges (Demosponges, Lubomirskiidae) dominate the fauna of the littoral zone of Lake Baikal. Over the last years, there have been mass diseases and death of endemic sponges. Previously, the strain Janthinobacterium sp. SLB01 was isolated from the diseased sponge Lubomirskia baicalensis. The studies of the pathogenicity of the strain Janthinobacterium sp. SLB01 for Baikal sponges has not been carried out. Therefore we infected experimentally in vitro to determine its pathogenicity by the cell culture of the primmorphs with subsequent isolation, sequencing, and analysis of the genomes. The purpose of the study is to show that the strain Janthinobacterium sp. SLB01 isolated from the diseased sponge L. baicalensis is a pathogen for the cell culture of primmorphs. The bacteria from the infected samples of the primmorphs were isolated and identified as strain Janthinobacterium sp. PLB02. A comparative analysis of the genomes of the strains Janthinobacterium sp. SLB01 and Janthinobacterium sp. PLB02 showed that they are practically identical. The genomes of both strains contain genes vioABCDE violacein, flok formation, and strong biofilm, and the type VI secretion system (T6SS), as the primary virulence factor. The bacterial strains Janthinobacterium sp. based on a comparison of complete genomes showed similarity with strain Janthinobacterium lividum MTR. Isolated our strains of Janthinobacterium sp. are pathogens for cell cultures of primmorphs and L. baicalensis sponges. The results of the study will help to expand the understanding of microbial relationships in the development of disease and the death of Baikal sponges.
Alternations of fecal microbes and lung tissue microbes in Lung Cancer patients is more consistent than that of sputum
Authors: Li Yanze , Zhang Hao , Kun Huang , Wang Zhaohui , Huang Kai
Published: December 2021

Microbiome in the human body environment is related to the occurrence of a variety of disease phenotypes. Recent studies discovered that lung is an open organism with in touch of air and microbe in it, and the presence of some microbes in lung cancer tissues proved that there are many microbes in lungs. In this project, we collected lung tissue, feces and sputum from three Bioprojects of NCBI related to lung cancer (LC). Each project contains LC cases and lung normal (LN) controls. Those three projects contain a total of 339 samples of 16s rRNA sequencing data. By analyzing the composition of microbes in the three environments, and predicting their functions we found that compared with sputum, the ecological environment of fecal microbe is closer to tissue microbes in terms of evolutionary relationship, indicating that the impact of feces on tissue microbes is greater than that of the sputum. We used Picrust2 to predict the differential microbe function of lung cancer (LC) and the control (Lung Normal, LN) groups in the three environments, and found that at the microbe genetic level, compared to feces and sputum, sputum and tissues, feces and tissues have more common Differential genes, at the level of differential enzyme genes and differential pathways, feces and tissues have more common differences compared to feces and sputum, sputum and tissues. Our results showed that the similarity of feces and tissue microbiome is closer than the similarity of sputum and feces microbe. Through Spearman correlation analysis based on the relative abundance of predicted pathways and the relative abundance of genus classified by LDA analysis as marker diseases and healthy samples. The results indicated that the activation of marker genus in sputum and feces and significantly changed pathways has an opposite trend, and there are many pathways contributing to glycolysis are correlated with marker genus. Patients with LC has potential to regulate the microbe composition of feces, tissues and sputum by regulating metabolism.
PIKfyve inhibition reveals a novel role for Inpp4b in the regulation of PtdIns(3)P and lysosome dynamics
Authors: Saffi Golam T. , Mangialardi Emily M. , Vacher Jean , Botelho Roberto J. , Salmena Leonardo
Published: December 2021

Lysosome membranes contain diverse phosphoinositide (PtdIns) lipids that co-ordinate lysosome function and dynamics. The PtdIns repertoire on lysosomes is tightly regulated by the action of diverse PtdIns kinases and phosphatases. Specific roles for PtdIns in lysosomal function and dynamics are currently unclear and require further investigation. PIKfyve, a lipid kinase which synthesizes PtdIns(3,5)P2 from PtdIns(3)P, controls lysosome “fusion-fission” cycles dynamics, autophagosome turnover and endocytic cargo delivery. We have recently characterized a role for INPP4B, a PtdIns phosphatase which hydrolyses PtdIns(3,4)P2 to form PtdIns(3)P, in the regulation of lysosomal biogenesis and function. To gain a better understanding of PtdIns homeostasis on lysosomes, we investigated the consequence of disrupting PIKfyve in Inpp4b-deficient mouse embryonic fibroblasts. Surprisingly, simultaneous inhibition of Inpp4b and PIKfyve functions impair lysosome “fission” dynamics and thereby exacerbate lysosome enlargement, inhibit autophagic flux. Further examination into the underlying processes that may explain exaggerated lysosome enlargement revealed elevated levels of lysosome associated PtdIns(3)P as contributing factors that control lysosome morphology in cells where Inpp4b and PIKfyve are disrupted. Overall, our study suggests that lysosomal functions are regulated by Inpp4b, through a paradoxical role in suppressing the induction of PtdIns(3)P production.

SUMMARY STATEMENT

In this study we identify a novel crosstalk between Inpp4b and PIKfyve. This crosstalk regulates lysosome membrane phosphoinositide composition and lysosomal homeostasis. Our data demonstrate that Inpp4b restricts VPS34-dependent induction of PtdIns(3)P levels, which is activated upon apilimod-mediated PIKfyve inhibition. Through this mechanism, Inpp4b contributes to the regulation of lysosomal membrane dynamics and homeostasis.
Human shape representations are not an emergent property of learning to classify objects
Authors: Malhotra Gaurav , Dujmović Marin , Hummel John , Bowers Jeffrey S
Published: December 2021

Humans are particularly sensitive to changes in the relationships between parts of objects. It remains unclear why this is. One hypothesis is that relational features are highly diagnostic of object categories and emerge as a result of learning to classify objects. We tested this by analysing the internal representations of supervised convolutional neural networks (CNNs) trained to classify large sets of objects. We found that CNNs do not show the same sensitivity to relational changes as previously observed for human participants. Furthermore, when we precisely controlled the deformations to objects, human behaviour was best predicted by the amount of relational changes while CNNs were equally sensitive to all changes. Even changing the statistics of the learning environment by making relations uniquely diagnostic did not make networks more sensitive to relations in general. Our results show that learning to classify objects is not sufficient for the emergence of human shape representations.
The loader complex Scc2/4 forms co-condensates with DNA as loading sites for cohesin
Authors: Zernia Sarah , Kamp Dieter , Stigler Johannes
Published: December 2021

The genome is organized by diverse packaging mechanisms like nucleosome formation, loop extrusion and phase separation, which all compact DNA in a dynamic manner. Phase separation additionally drives protein recruitment to condensed DNA sites and thus regulates gene transcription. The cohesin complex is a key player in chromosomal organization that extrudes loops to connect distant regions of the genome and ensures sister chromatid cohesion after S-phase. For stable loading onto the DNA and for activation, cohesin requires the loading complex Scc2/4. As the precise loading mechanism remains unclear, we investigated whether phase separation might be the initializer of the cohesin recruitment process. We found that, in absence of cohesin, budding yeast Scc2/4 forms phase separated co-condensates with DNA, which comprise liquid-like properties shown by droplet shape, fusion ability and reversibility. We reveal in DNA curtain and optical tweezer experiments that these condensates are built by DNA bridging and bending through Scc2/4. Importantly, Scc2/4-mediated condensates recruit cohesin efficiently and increase the stability of the cohesin complex. We conclude that phase separation properties of Scc2/4 enhance cohesin loading by molecular crowding, which might then provide a starting point for the recruitment of additional factors and proteins.
Impact of contamination on biology, biochemical, and histology ofEobania vermiculataandMonacha obstructaduring different seasons in Ismailia, Egypt
Authors: Abd El mageed Yassmeen S. M. , Ali Ghobashy Abd El Fattah , Al-Thomali Asma W. , Soliman Maha F. M. , Mohammadein Amaal , El-Shenawy Nahla S.
Published: December 2021

Land snails are found to be an appropriate sentinel organism, and the biomarkers chosen are effective for terrestrial heavy metal biomonitoring. The study aimed to compare the biological, biochemistry, and histology of two land snails in the Ismailia governorate, Egypt during different seasons. Random snails were collected from January 2015 to December 2015 from two sites in the Ismailia Governorate, on wet days during each season’s middle month. Soft tissues were taken from the dissected snails. It was noticed that most of the morphometric parameters measured shell height (ShH), last whorl width (LWW), maximum diameter (MaxD), aperture height (AH), and aperture width (AW) were higher inEobania vermiculata(Sp. 1) than those measured inMonacha obstructa(Sp. 2), except for shell height measurement, which was the same in both species. The growth rate of Sp. 1 and Sp. 2 changed seasonally. In the more polluted areas with heavy metals, lipid peroxidation (LPO) was higher in snails and total protein content than in the snails collected from the less polluted areas for all seasons. However, the snails displayed lower levels of glutathione (GSH) as compared to snails at a less polluted site. GSH and LPO levels, on the other hand, have a negative relationship between them. Histopathological alterations in the digestive gland were more obvious in the general architecture of the digestive gland that had lost its tubular appearance. The excretory cells showed an increase in their excretory granules’ number and size while calcium cells decreased. Also, gonad follicles have lost their normal architecture with the degeneration of some stages of spermatogenesis and oogenesis. In conclusion, There was a strong correlation between GSH levels and total protein content in the same soft tissues. GSH and LPO levels, on the other hand, have a negative relationship. The overall results display the usefulness ofE. vermiculataandM. obstructaland snails as bioindicator organisms and support the application of this ecotoxicological approach for evaluating the biologic impact of toxins.E. vermiculatais more abundant thanM. obstructa. The density, morphometric, biochemical, and histology ofE. vermiculataandM. obstructawere different at different seasons.
Striking Antibody Evasion Manifested by the Omicron Variant of SARS-CoV-2
Authors: Liu Lihong , Iketani Sho , Guo Yicheng , Chan Jasper F-W. , Wang Maple , Liu Liyuan , Luo Yang , Chu Hin , Huang Yiming , Nair Manoj S. , Yu Jian , Chik Kenn K-H. , Yuen Terrence T-T. , Yoon Chaemin , To Kelvin K-W. , Chen Honglin , Yin Michael T. , Sobieszczyk Magdalena E. , Huang Yaoxing , Wang Harris H. , Sheng Zizhang , Yuen Kwok-Yung , Ho David D.
Published: December 2021

The Omicron (B.1.1.529) variant of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) was only recently detected in southern Africa, but its subsequent spread has been extensive, both regionally and globally1. It is expected to become dominant in the coming weeks2, probably due to enhanced transmissibility. A striking feature of this variant is the large number of spike mutations3 that pose a threat to the efficacy of current COVID-19 (coronavirus disease 2019) vaccines and antibody therapies4. This concern is amplified by the findings from our study. We found B.1.1.529 to be markedly resistant to neutralization by serum not only from convalescent patients, but also from individuals vaccinated with one of the four widely used COVID-19 vaccines. Even serum from persons vaccinated and boosted with mRNA-based vaccines exhibited substantially diminished neutralizing activity against B.1.1.529. By evaluating a panel of monoclonal antibodies to all known epitope clusters on the spike protein, we noted that the activity of 17 of the 19 antibodies tested were either abolished or impaired, including ones currently authorized or approved for use in patients. In addition, we also identified four new spike mutations (S371L, N440K, G446S, and Q493R) that confer greater antibody resistance to B.1.1.529. The Omicron variant presents a serious threat to many existing COVID-19 vaccines and therapies, compelling the development of new interventions that anticipate the evolutionary trajectory of SARS-CoV-2.
Learning Single-Cell Perturbation Responses using Neural Optimal Transport
Authors: Bunne Charlotte , Stark Stefan G. , Gut Gabriele , del Castillo Jacobo Sarabia , Lehmann Kjong-Van , Pelkmans Lucas , Krause Andreas , Rätsch Gunnar
Published: December 2021

The ability to understand and predict molecular responses towards external perturbations is a core question in molecular biology. Technological advancements in the recent past have enabled the generation of high-resolution single-cell data, making it possible to profile individual cells under different experimentally controlled perturbations. However, cells are typically destroyed during measurement, resulting in unpaired distributions over either perturbed or non-perturbed cells. Leveraging the theory of optimal transport and the recent advents of convex neural architectures, we learn a coupling describing the response of cell populations upon perturbation, enabling us to predict state trajectories on a single-cell level. We apply our approach, CellOT, to predict treatment responses of 21,650 cells subject to four different drug perturbations. CellOT outperforms current state-of-the-art methods both qualitatively and quantitatively, accurately capturing cellular behavior shifts across all different drugs.
Determining the effects of training duration on the behavioral expression of habitual control in humans: a multilaboratory investigation
Authors: Pool Eva R. , Gera Rani , Fransen Aniek , Perez Omar D. , Cremer Anna , Aleksic Mladena , Tanwisuth Sandy , Quail Stephanie , Ceceli Ahmet O. , Manfredi Dylan A. , Nave Gideon , Tricomi Elizabeth , Balleine Bernard , Schonberg Tom , Schwabe Lars , O'Doherty John P.
Published: December 2021

It has been suggested that there are two distinct and parallel mechanisms for controlling instrumental behavior in mammals: goal-directed actions and habits. To gain an understanding of how these two systems interact to control behavior, it is essential to characterize the mechanisms by which the balance between these systems is influenced by experience. Studies in rodents have shown that the amount of training governs the relative expression of these two systems: Behavior is goal-directed following moderate training, but the more extensively an instrumental action is trained, the more it becomes habitual. It is less clear whether humans exhibit similar training effects on the expression of goal-directed and habitual behavior, as human studies have reported contradictory findings. To tackle these contradictory findings, we formed a consortium, where four laboratories undertook a preregistered experimental induction of habits by manipulating the amount of training. There was no statistical evidence for a main effect of the amount of training on the formation and expression of habits. However, exploratory analyses suggest a moderating effect of the affective component of stress on the impact of training over habit expression. Participants who were lower in affective stress appeared to be initially goal-directed, but became habitual with increased training, whereas participants who were high in affective stress were already habitual even after moderate training, thereby manifesting insensitivity to overtraining effects. Our findings highlight the importance of the role of moderating variables such as individual differences in stress and anxiety when studying the experimental induction of habits in humans.
Spectroscopic evaluation of UVI–cement mineral interactions: ettringite and hydrotalcite
Authors: Yorkshire Antonia S. , Stennett Martin C. , Walkley Brant , O'Sullivan Sarah E. , Mottram Lucy M. , Bailey Daniel J. , Provis John L. , Hyatt Neil C. , Corkhill Claire L.
Published: December 2021

Portland cement based grouts used for radioactive waste immobilization contain high replacement levels of supplementary cementitious materials, including blast-furnace slag and fly ash. The minerals formed upon hydration of these cements may have capacity for binding actinide elements present in radioactive waste. In this work, the minerals ettringite (Ca6Al2(SO4)3(OH)12·26H2O) and hydrotalcite (Mg6Al2(OH)16CO3·4H2O) were selected to investigate the importance of minor cement hydrate phases in sequestering and immobilizing UVI from radioactive waste streams. U L
III-edge X-ray absorption spectroscopy (XAS) was used to probe the UVI coordination environment in contact with these minerals. For the first time, solid-state 27Al magic angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy was applied to probe the Al coordination environment in these UVI-contacted minerals and make inferences on the UVI coordination, in conjunction with the X-ray spectroscopy analyses. The U L
III-edge XAS analysis of the UVI-contacted ettringite phases found them to be similar (>∼70%) to the uranyl oxyhydroxides present in a mixed becquerelite/metaschoepite mineral. Fitting of the EXAFS region, in combination with 27Al NMR analysis, indicated that a disordered Ca- or Al-bearing UVI secondary phase also formed. For the UVI-contacted hydrotalcite phases, the XAS and 27Al NMR data were interpreted as being similar to uranyl carbonate, that was likely Mg-containing.
Building resilience in retail supply chains: Lessons learned from COVID-19 and future pathways
Authors: Butt Atif Saleem
Published: December 2021

Purpose

This study explores the countermeasures taken by retailers to mitigate the effects of COVID-19 on supply chain disruptions.

Design/methodology/approach

This research uses a multiple case study approach and undertakes 36 semi-structured interviews with senior management of the four largest retailers of the United Arab Emirates. The respondents were designated at different positions such as Vice President, Director and Project Manager.

Findings

Results reveal that retailers are employing six countermeasures to mitigate the effects of COVID-19 on supply chains. Particularly, retailers are securing required demand, preserving cash flows, redirecting inventory, adding capacity to their distribution centres, becoming more flexible with their direct or third-party logistics provider and finally widening delivery options for their suppliers to mitigate the impact of COVID-19.

Research limitations/implications

This study has some limitations. First, the results of this study cannot be generalized to a broader population as it attempts to build an initial theory. Second, this study uses a cross-sectional approach to explore the countermeasures employed by retailing firms to mitigate the effects of COVID-19.

Originality/value

A notable weakness in a supply chain disruption literature is an unfulfilled need for research examining the strategies employed by retailers to respond to/address the challenges posed by COVID-19. Our study fills this gap.
Changes in the effect of credence cues on restaurant delivery service under different health risks
Authors: Kim Jewoo , Kim Jaewook , Wang Yiqi
Published: December 2021

Purpose

Due to increased health concerns, restaurant customers rely more on credible cues that indirectly represent health-related credence quality. To comprehensively understand the dynamics between credence cues and restaurant delivery with different infection risks, this study aims to investigate changes in cue utilization during the pandemic.

Design/methodology/approach

Data on delivery sales, brand and review rating between 2019 and the first half of 2020 were obtained from Meituan. Fixed-effects estimation was used to investigate 579,858 restaurant observations across 338 cities in China.

Findings

Health concerns significantly increased the use of restaurant delivery and the increased delivery sales remained steady even after infection risk was reduced. However, cue utilization in restaurant delivery substantially changed depending on inflection risk. In the pandemic-spreading period, the sales effect of the brand increased while that of review rating decreased. The decreased effect of review rating was recovered in the pandemic-flattening period, whereas the abnormal brand effect continued only when branded restaurants had a high rating.

Research limitations/implications

The findings demonstrate the selective and contextual nature of cue utilization in the restaurant delivery setting. These characteristics are also manifested in a health crisis from a credence cue perspective.

Practical implications

The findings demonstrate the selective and contextual nature of cue utilization in the restaurant delivery setting. These characteristics are also manifested in a health crisis from a credence cue perspective. Further, this study re-conceptualizes credence quality and cues, considering their roles in risk management. The findings help develop risk management strategies based on customers’ usage patterns of credence cues in health crises.

Originality/value

The dynamics between credence cues and restaurant delivery has not been comprehensively investigated, especially when infection risk changes. This study delivers theoretical and practical contributions about how to use credence cues in the restaurant business amid health crises.
The impact of asymmetric perceptions of buyer-supplier governance mechanisms on relational rents
Authors: Vanpoucke Evelyne , Wetzels Martin , Rozemeijer Frank , Pilzak-Blonska Marion
Published: December 2021

Purpose

Buyers and suppliers often perceive relationship governance mechanisms, such as trust and contractual fairness, in different ways. These differences in perception create an extra layer of complexity that is often ignored in the extant literature. This study adds to the understanding of how perceived asymmetries in trust and contractual fairness, two key relationship governance mechanisms, impact relational rents. This study also analyzes how boundary spanners aid managers to deal with these perceived asymmetries.

Design/methodology/approach

Based on survey data of 103 buyer–supplier dyads from a single global manufacturer of industrial equipment, the authors test hypotheses of perceived asymmetries in trust and contractual fairness, as well as the moderating effect of boundary spanners, on relational rents.

Findings

This research challenges the belief that asymmetries negatively impact or lead to unstable buyer–supplier relationships. Furthermore, it explains how preferential treatment and length of the relationship could reduce the impact of asymmetric perceptions.

Practical implications

This study stresses that open communication, which considers different viewpoints, helps to overcome the negative differences in attitude and perception. In addition, the authors found that long-term relationships seem to be far more resilient in dealing with asymmetries and that preferential treatments are best applied in (approximately) symmetric relationships in terms of contractual fairness.

Originality/value

While studies on buyer–supplier relationships often assume symmetric perceptions of governance mechanisms, asymmetric perceptions are far more prominent in reality. This study aims to improve one’s understanding of the impact of these asymmetries as well as how boundary spanners can affect these perceptions.
Visitation and quality of life among older adults in jail
Authors: Prost Stephanie Grace , Novisky Meghan A.
Published: December 2021

Purpose

The purpose of this paper aims to examine differences in measures of and relationships between visitation and quality of life (QOL) among older and younger jailed adults. The authors also explored the contribution of visitation to QOL among adults in this setting. The authors anticipated fewer visits and lower QOL among older adults. Framed by psychosocial developmental theory, the authors also anticipated a larger effect in the relationship between visitation and QOL among older rather than younger adults and that visitation would contribute most readily to psychological QOL.

Design/methodology/approach

Cross-sectional data from a large US jail were used (n = 264). The authors described the sample regarding visitation and QOL measures among older (≥45) and younger adults (≤44) and examined differences in measures of and relationships between visitation and QOL using independent sample t-tests and bivariate analyses. The authors explored the contribution of visitation to psychological, social relationships, physical and environmental QOL among jailed adults using hierarchical multiple linear regression.

Findings

Older adults had fewer family visits and lower physical QOL than younger adults, disparities were moderate in effect (d range = 0.33–0.35). A significant difference also emerged between groups regarding the visitation and environmental QOL relationship (z = 1.66, p <0.05). Visitation contributed to variation in physical and social relationships QOL among jailed adults (Beta range = 0.19–0.24).

Originality/value

Limited research exists among jailed older adults and scholars have yet to examine the relationship between visitation and QOL among persons in these settings.
Earnings management and issue characteristics: an empirical analysis of IPOs in India
Authors: Mangala Deepa , Dhanda Mamta
Published: December 2021

Purpose

This study aims to examine earnings management around initial public offerings (IPOs) in India. It also explores the influence of issue characteristics on earnings management around the IPOs.

Design/methodology/approach

A sample of 511 IPOs that came during April 2003-March 2019 is studied for calculating earnings management for pre-issue, issue and post-issue years. Using Cross-Sectional Modified Jones Model, the paper presents earnings management on the basis of three proxies i.e. discretionary accruals, discretionary current accruals and discretionary long-term accruals. The influence of issue characteristics on earnings management practised around the IPOs is also observed through correlation and multiple regression analysis.

Findings

The paper finds that earnings management is abnormally high during the issue year compared with pre-issue and post-issue years. It also unveils that profitability, premium, age, and size of the issuer significantly determine the level of pre-issue and issue year earnings management practised by Indian IPO issuers.

Research limitations/implications

The findings are useful to stakeholders (potential investors, analysts and regulators) to observe, assess and understand the quality of financial numbers that are based on fallacious disclosure of accounting figures. It provides insight into the possibilities of managed earnings around the issue that could influence investors’ decision-making. Further, the study reflects the efficacy of Indian regulatory norms for IPOs.

Originality/value

To the authors’ knowledge, it is the only Indian study that had used an extensive data set of about two decades to calculate earnings management during pre-issue, issue and post-issue years. The uniqueness of the study further lies in three proxies of earnings management representing short-term and long-term accruals. Moreover, it is the first study to observe the influence of IPO issue characteristics on earnings management.