bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acceptability, Usability, and Performance of Lateral Flow Immunoassay Tests for Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies: REACT-2 Study of Self-Testing in Nonhealthcare Key Workers
Authors: Davies Bethan , Araghi Marzieh , Moshe Maya , Gao He , Bennet Kimberly , Jenkins Jordan , Atchison Christina , Darzi Ara , Ashby Deborah , Riley Steven , Barclay Wendy , Elliott Paul , Ward Helen , Cooke Graham 
Published: October 2021

Abstract

Background
Seroprevalence studies are essential to understand the epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Various technologies, including laboratory assays and point-of-care self-tests, are available for antibody testing. The interpretation of seroprevalence studies requires comparative data on the performance of antibody tests.

Methods
In June 2020, current and former members of the United Kingdom police forces and fire service performed a self-test lateral flow immunoassay (LFIA), had a nurse-performed LFIA, and provided a venous blood sample for enzyme-linked immunosorbent assay (ELISA). We present the prevalence of antibodies to SARS-CoV-2 and the acceptability and usability of self-test LFIAs, and we determine the sensitivity and specificity of LFIAs compared with laboratory ELISA.

Results
In this cohort of 5189 current and former members of the police service and 263 members of the fire service, 7.4% (396 of 5348; 95% confidence interval [CI], 6.7–8.1) were antibody positive. Seroprevalence was 8.9% (95% CI, 6.9–11.4) in those under 40 years, 11.5% (95% CI, 8.8–15.0) in those of nonwhite ethnicity, and 7.8% (95% CI, 7.1–8.7) in those currently working. Self-test LFIA had an acceptability of 97.7% and a usability of 90.0%. There was substantial agreement between within-participant LFIA results (kappa 0.80; 95% CI, 0.77–0.83). The LFIAs had a similar performance: compared with ELISA, sensitivity was 82.1% (95% CI, 77.7–86.0) self-test and 76.4% (95% CI, 71.9–80.5) nurse-performed with specificity of 97.8% (95% CI, 97.3–98.2) and 98.5% (95% CI, 98.1–98.8), respectively.

Conclusions
A greater proportion of this nonhealthcare key worker cohort showed evidence of previous infection with SARS-CoV-2 than the general population at 6.0% (95% CI, 5.8–6.1) after the first wave in England. The high acceptability and usability reported by participants and similar performance of self-test and nurse-performed LFIAs indicate that the self-test LFIA is fit for purpose for home testing in occupational and community prevalence studies.
Evaluation of the anti-biofilm activities of bacterial cellulose-tannic acid-magnesium chloride composites using an in vitro multispecies biofilm model
Authors: He Wei , Zhang Zhaoyu , Chen Jing , Zheng Yudong , Xie Yajie , Liu Wenbo , Wu Jian , Mosselhy Dina A 
Published: October 2021

Abstract
Chronic wounds are a serious worldwide problem, which are often accompanied by wound infections. In this study, bacterial cellulose (BC)-based composites introduced with tannic acid (TA) and magnesium chloride (BC-TA-Mg) were fabricated for anti-biofilm activities. The prepared composites’ surface properties, mechanical capacity, thermal stability, water absorption and retention property, releasing behavior, anti-biofilm activities and potential cytotoxicity were tested. Results showed that TA and MgCl2 particles closely adhered to the nanofibers of BC membranes, thus increasing surface roughness and hydrophobicity of the membranes. While the introduction of TA and MgCl2 did not influence the transparency of the membranes, making it beneficial for wound inspection. BC-TA and BC-TA-Mg composites displayed increased tensile strength and elongation at break compared to pure BC. Moreover, BC-TA-Mg exhibited higher water absorption and retention capacity than BC and BC-TA, suitable for the absorption of wound exudates. BC-TA-Mg demonstrated controlled release of TA and good inhibitory effect on both singly cultured Staphylococcus aureus and Pseudomonas aeruginosa biofilm and co-cultured biofilm of S. aureus and P. aeruginosa. Furthermore, the cytotoxicity grade of BC-TA-6Mg membrane was eligible based on standard toxicity classifications. These indicated that BC-TA-Mg is potential to be used as wound dressings combating biofilms in chronic wounds.
‘Everyone seems to be agreeing at the minute that face-to-face is the way forward’: practitioners’ perspectives on post-pandemic mathematics and statistics support
Authors: Gilbert Holly , Hodds Mark , Lawson Duncan 
Published: October 2021

Abstract
Mathematics and statistics support (MSS) is now firmly embedded in the learning and teaching infra-structure of most UK universities and in many universities worldwide. In common with other higher education activities, in response to restrictions put in place to reduce the spread of Covid-19, MSS transitioned rapidly to online delivery in spring 2020. This paper reports on thinking within the practitioner community about good practice in the delivery of online MSS. A two-phase approach was used to collect this shared wisdom: an initial questionnaire in May 2020 (just after provision had moved online) and interviews with practitioners in January/February 2021 after colleagues had some experience in online provision and had had the opportunity to reflect on and modify the measures hastily put in place in spring 2020. The focus of the study is not only on what is currently being provided but also on what MSS will look like once all pandemic related restrictions have been ended. The overall feeling of the participants is that face-to-face MSS will return as the dominant form of delivery but that the benefits of online provision are such that a significant minority of provision will remain in this form.
Circadian regulation of the transcriptome in a complex polyploid crop
Authors: Rees Hannah , Rusholme-Pilcher Rachel , Bailey Paul , Colmer Joshua , White Benjamen , Reynolds Connor , Ward Sabrina Jaye , Graham Calum A. , Dantas Luíza Lane de Barros , Dodd Antony N. , Hall Anthony 
Published: October 2021

AbstractThe circadian clock is a finely balanced time-keeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of three homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific sub-genome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes are largely conserved between wheat and Arabidopsis, however striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs, and identifies clock-controlled pathways that might provide important targets for future wheat breeding.
An exploratory analysis of 4844 withdrawn articles and their retraction notes
Authors: Toma Catalin , Padureanu Liliana 
Published: October 2021

AbstractThe objective of our study was to obtain an updated image of the dynamic of retractions and retraction notes, retraction reasons for questionable research and publication practices, countries producing retracted articles, and the scientific impact of retractions by studying 4844 PubMed indexed retracted articles published between 2009 and 2020 and their retraction notes.RESULTSMistakes/inconsistent data account for 32% of total retractions, followed by images(22,5%), plagiarism(13,7%) and overlap(11,5%).Thirty countries account for 94,79% of 4844 retractions. Top five are: China(32,78%), United States(18,84%), India(7,25%), Japan(4,37%) and Italy(3,75%).The total citations number for all articles is 140810(Google Scholar), 96000(Dimensions).Average exposure time(ET) is 28,89 months. Largest ET is for image retractions(49,3 months), lowest ET is for editorial errors(11,2 months).The impact of retracted research is higher for Spain, Sweden, United Kingdom, United States, and other nine countries and lower for Pakistan, Turkey, Malaysia, and other six countries, including China.CONCLUSIONSMistakes and data inconsistencies represent the main retraction reason; images and ethical issues show a growing trend, while plagiarism and overlap still represent a significant problem. There is a steady increase in QRP and QPP article withdrawals. Retraction of articles seems to be a technology-dependent process.The number of citations of retracted articles shows a high impact of papers published by authors from certain countries. The number of retracted articles per country does not always accurately reflect the scientific impact of QRP/QPP articles.The country distribution of retraction reasons shows structural problems in the organization and quality control of scientific research, which have different images depending on geographical location, economic development, and cultural model.
In vitro Anti-Cancer Activity of Oliveria decumbens Vent. Extract, an Endemic Persian Medicinal Plant, on HT-29 Colorectal Cancer Cell Line
Authors: Khodavirdipour Amir , Haddadi Fatemeh , nejad Hamideh Rouhani , Shiri Yasoub , Tilak Veronica Preetha 
Published: October 2021

AbstractIntroductionThe top 3 causes of death worldwide include heart disease, injury, and cancer; and cancer records the 2nd place as the leading cause of death in the United States of America after cardiovascular diseases and injuries. Cancer can begin and progress in a very highly twisted and complex pattern and follow the multifactorial route. There is only very few research on medicinal properties Oliveria decumbens rare and valuable plant specially on cancer. So, in this study we tried to cover all needs for future in vivo research.MethodsMTT assay has been performed to estimate the cytotoxicity of the ethanolic extract of the plant. Its free radical capacity evaluation was done by DPPH assay. Furthermore, real-time PCR, the wound-healing assay along with a DNA damage test to study DNA fragmentation characteristics. The plant’s transcriptomic study was performed by NGS de Novo assembly.ResultOliveria decumbens ethanolic extract showed an Ic50 of 14.39 μg/ml. The real-time PCR showed that Oliveria decumbens ethanolic extract significantly induced apoptosis by upregulating the bax gene and slight downregulation of bcl2 an anti-apoptosis gene. The NGS de Novo transcriptome analysis discovered 38 genes responsible for secondary metabolite synthesis so far. The remaining genes and reconstruction of the co-expression network of the transcriptome are underway.ConclusionThe outcome of the Scratch-test and DNA fragmentation confirmed the anti-metastatic and DNA damage properties respectively. Based on these findings; Oliveria decumbens ethanolic extract shall be considered as potential anticancer and chemotherapeutic agents which may elucidate in upcoming studies.
CHD8 regulates gut epithelial cell function and affects autism-related behaviours through the gut-brain axis
Authors: Chatterjee Ipsita , Getselter Dimitry , Ghaneem Nasreen , Bel Shai , Elliott Evan 
Published: October 2021

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by early onset deficits in social behavior and repetitive behavior. Chromodomain helicase DNA binding protein (CHD8) is one of the genes with the strongest association to autism. Alongside with the core symptoms of ASD, individuals with ASD are reported to have gastrointestinal (GI) problems, and a majority of individuals with CHD8 mutations display GI problems. However, the relationship between autism related genes, such as CHD8, gastrointestinal function, and autism related behaviours are yet very unclear. In the current study, we found that mice haploinsufficient for CHD8 have leaky gut, a dysregulated transcriptome in gut epithelial cells, decreased gut tuft cells and goblet cells, and an increase in microbial load. Specific deletion of CHD8 in gut epithelial cells induced an increase in anxiety-related behaviours in, a phenotype that is often observed in autism and full body knockdown of CHD8, in addition to decreased tuft cells. In addition, antibiotic treatment of CHD8 haploinsufficient mice attenuates sociability deficits. Therefore, the current study determines a pathway for autism-related GI deficits, and how these deficits may play a direct role in the development of autism-related behaviours.
Neural language processing across time, space, frequency and age: MEG-MVPA classification of intertrial phase coherence
Authors: Jensen Mads , Hyder Rasha , Westner Britta U. , Højlund Andreas , Shtyrov Yury 
Published: October 2021

AbstractLanguage is a key part of human cognition. Whereas many neurocognitive abilities decline with age, for language the picture is much less clear and how exactly language processing changes with aging is still unknown. To investigate this, we employed magnetoencephalography (MEG) and recorded neuromagnetic brain responses to auditory linguistic stimuli in healthy participants of younger and older age using a passive task-free paradigm and a range of different linguistic stimulus contrasts, which enabled us to assess neural language processes at multiple levels (lexical, semantic, morphosyntactic). By using machine learning-based classification algorithms to scrutinise intertrial phase coherence of MEG responses in source space, we found significant differences between younger and older participants across several frequency bands and for all tested processing types, which shows multiple changes in the brain’s neurolinguistic circuits which may be due to both healthy aging in general and compensatory processes in particular.
Le Petit Prince: A multilingual fMRI corpus using ecological stimuli
Authors: Li Jixing , Bhattasali Shohini , Zhang Shulin , Franzluebbers Berta , Luh Wen-Ming , Spreng R. Nathan , Brennan Jonathan R. , Yang Yiming , Pallier Christophe , Hale John 
Published: October 2021

ABSTRACTNeuroimaging using more ecologically valid stimuli such as audiobooks has advanced our understanding of natural language comprehension in the brain. However, prior naturalistic stimuli have typically been restricted to a single language, which limited generalizability beyond small typological domains. Here we present theLe Petit PrincefMRI Corpus (LPPC–fMRI), a multilingual resource for research in the cognitive neuroscience of speech and language during naturalistic listening (Open-Neuro: ds003643). 49 English speakers, 35 Chinese speakers and 28 French speakers listened to the same audiobookThe Little Princein their native language while multi-echo functional magnetic resonance imaging was acquired. We also provide time-aligned speech annotation and word-by-word predictors obtained using natural language processing tools. The resulting timeseries data are shown to be of high quality with good temporal signal-to-noise ratio and high inter-subject correlation. Data-driven functional analyses provide further evidence of data quality. This annotated, multilingual fMRI dataset facilitates future re-analysis that addresses cross-linguistic commonalities and differences in the neural substrate of language processing on multiple perceptual and linguistic levels.
Systematic discovery of mutation-directed neo-protein-protein interactions in cancer
Authors: Mo Xiulei , Niu Qiankun , Ivanov Andrey A. , Tsang Yiu Huen , Tang Cong , Shu Changfa , Wahafu Alafate , Doyle Sean P. , Cicka Danielle , Yang Xuan , Fan Dacheng , Reyna Matthew A. , Cooper Lee A.D. , Moreno Carlos S. , Zhou Wei , Owonikoko Taofeek , Lonial Sagar , Khuri Fadlo R. , Du Yuhong , Ramalingam Suresh S. , Mills Gordon B. , Fu Haian 
Published: October 2021

SUMMARYComprehensive sequencing of patient tumors reveals numerous genomic mutations across tumor types that enable tumorigenesis and progression. A subset of oncogenic driver mutations results in neomorphic activity where the mutant protein mediates functions not engaged by the parental molecule. Here, we identify prevalent variant-enabled neomorph-protein-protein interactions (neoPPI) with a quantitative High Throughput differential Screening (qHT-dS) platform. Coupling of highly sensitive BRET biosensors with miniaturized co-expression in an ultra-HTS format allows large-scale monitoring of interactions of wild-type and mutant variant counterparts with a library of cancer-associated proteins in live cells. Screening of 13,392 interactions with 1,474,560 data points revealed a landscape of gain-of-interactions encompassing both oncogenic and tumor suppressor mutations. For example, the recurrent BRAF V600E lesion mediates KEAP1 neoPPI, rewiring a BRAFV600E-KEAP1 signaling axis and creating collateral vulnerability to NQO1 substrates, offering a combination therapeutic strategy. Thus, cancer genomic alterations can create neo-interactions, informing variant-directed therapeutic approaches for precision medicine.
AIM2 inflammasome activation in astrocytes occurs during the late phase of EAE
Authors: Barclay William E. , Deerhake M. Elizabeth , Inoue Makoto , Nonaka Toshiaki , Nozaki Kengo , Luzum Nathan A. , Aggarwal Nupur , Miao Edward A. , Shinohara Mari L. 
Published: October 2021

ABSTRACTInflammasomes are a class of innate immune signaling platforms that activate in response to an array of cellular damage and pathogens. Inflammasomes promote inflammation under many circumstances to enhance immunity against pathogens and inflammatory responses through their effector cytokines, IL-1β and IL-18. Multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE), are such autoimmune conditions influenced by inflammasomes. Despite work investigating inflammasomes during EAE, little remains known concerning the role of inflammasomes in the central nervous system (CNS) during the disease. Here we use multiple genetically modified mouse models to monitor activated inflammasomesin situbased on ASC oligomerization in the spinal cord. Using inflammasome reporter mice, we found heightened inflammasome activation in astrocytes after the disease peak. In contrast, microglia and CNS-infiltrated myeloid cells had few activated inflammasomes in the CNS during EAE. Astrocyte inflammasome activation was dependent on AIM2, but low IL-1β expression and no significant signs of cell death were found in astrocytes during EAE. Thus, the AIM2 inflammasome activation in astrocytes may have a distinct role from traditional inflammasome-mediated inflammation.SIGNIFICANCE STATEMENTInflammasome activation in the peripheral immune system is pathogenic in multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE). However, inflammasome activity in the central nervous system (CNS) is largely unexplored. Here, we used genetically modified mice to determine inflammasome activation in the CNS during EAE. Our data indicated heightened AIM2 inflammasome activation in astrocytes after the disease peak. Unexpectedly, neither CNS-infiltrated myeloid cells nor microglia were the primary cells with activated inflammasomes in SC during EAE. Despite AIM2 inflammasome activation, astrocytes did not undergo apparent cell death and produced little of the proinflammatory cytokine, IL-1β, during EAE. This study showed that CNS inflammasome activation occurs during EAE without associating with IL-1β-mediated inflammation.
Immunometabolic hijacking of immune cells by a Pseudomonas aeruginosa quorum-sensing signal
Authors: Bandyopadhaya Arunava , Singh Vijay K , Chakraborty Arijit , Tzika A. Aria , Rahme Laurence G 
Published: October 2021

AbstractMacrophages utilize metabolic pathways to generate energy and metabolites that may be vulnerable to pathogen hijacking to favor pathogen survival and persistence. It is unclear how bacterial pathogens alter metabolic pathways in immune cells for their benefit and persistence in the infected host. We have shown that the Pseudomonas aeruginosa quorum sensing (QS) signal molecule 2-aminoacetophenone (2-AA) allows pathogen persistence in host tissues by triggering host tolerization via histone deacetylase (HDAC)1-mediated epigenetic reprogramming. Here, we provide strong evidence that 2-AA-meditated persistence is linked to specific metabolic pathway alterations that reduce energy availability and biosynthetic macromolecules involved in host immune responses. 2-AA promotes a Warburg-like metabolic reprogramming effect, thereby increasing levels of lactate, which repressed inflammatory signaling in macrophages. Moreover, it interferes with pyruvate translocation to mitochondria, reducing mitochondrial (mt)-oxidative phosphorylation (OXPHOS) due to down-regulation of estrogen-regulated receptor (ERR)α and mitochondrial pyruvate carrier (MPC)-1. This metabolic reprogramming dampened energy production, reduced the acetyl-CoA pool, and generated an anti-inflammatory milieu that favors P. aeruginosa persistence. These findings provide evidence of first-in-class metabolic reprogramming in immune cells mediated by a QS signaling molecule. The specific metabolic programs affected provide insights that may guide the design and development of therapeutics and protective interventions against pathogen-induced immunometabolic alterations and persistence factors.
Polyvinyl Chloride Degradation by Intestinal Klebsiella of Pest larvae
Authors: Zhe Zhang , Peng Haoran , Yang Dongchen , Zhang Guoqing , Zhang Jinlin , Ju Feng 
Published: October 2021

AbstractMicrobial degradation of polyvinyl chloride (PVC) is eco-friendly and economically attractive but extremely challenging due to the lack of a molecular understanding of the degrading strains and enzymes. Motivated by the serendipitous discovery that the larva of an agricultural invasive insect pest, Spodoptera frugiperda, effectively survived PVC film alone, we profiled the intestinal microbiota of S. frugiperda larva and screened for PVC-degrading strains. Feeding on PVC film significantly changed the larval intestinal microbiota through selective enrichment of Enterococcus, Ochrobactrum, Falsochrobactrum, Microbaterium, Sphingobacterium and Klebsiella. From the larval intestine, we isolated the biofilm-forming Klebsiella sp. EMBL-1 and experimentally verified it as the first Klebsiella bacterium known to actively degrade and utilize PVC by various classic physicochemical and morphological analyses. We further used multiomic analyses, complementarily integrating genomic, transcriptomic, proteomic, and metabolomic insights, to identify enzyme-coding genes responsible for PVC degradation and proposed a biodegradation pathway for the bacterial strain. Overall, both S. frugiperda and strain EMBL-1 are first found to survive effectively on PVC film by using the polymer as the sole energy source. Moreover, this work exemplifying PVC biodegradation provides a reference for discovering more microbes and enzymatic resources for degrading other recalcitrant plastics.