bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient-derived triple negative breast cancer organoids provide robust model systems that recapitulate tumor intrinsic characteristics
Authors: Bhatia Sonam , Kramer Melissa , Russo Suzanne , Naik Payal , Arun Gayatri , Brophy Kyle , Andrews Peter , Fan Cheng , Perou Charles M. , Preall Jonathan , Ha Taehoon , Plenker Dennis , Tuveson David A. , Rishi Arvind , Wilkinson J Erby , McCombie W. Richard , Kostroff Karen , Spector David L. 
Published: August 2021

AbstractTriple negative breast cancer (TNBC) is an aggressive form of breast cancer with poor patient outcomes, and an unmet clinical need for targeted therapies and better model systems. Here, we developed and comprehensively characterized a diverse biobank of normal and breast cancer patient-derived organoids (PDOs) with a focus on TNBCs. PDOs recapitulated patient tumor intrinsic properties and a subset of PDOs can be propagated for long-term culture (LT-TNBCs). Single cell profiling of PDOs identified cell types and gene candidates affiliated with different aspects of cancer progression. The LT-TNBC organoids exhibit signatures of aggressive MYC-driven basal-like breast cancers and are largely comprised of luminal progenitor (LP)-like cells. The TNBC LP-like cells are distinct from normal LPs and exhibit hyperactivation of NOTCH and MYC signaling. Overall, our study validates TNBC PDOs as robust models for understanding breast cancer biology and progression, paving the way for personalized medicine and tailored treatment options.Statement of SignificanceA comprehensive analysis of TNBC patient-derived organoids is presented by genomic, transcriptomic, and in-vivo analyses, providing insights into cellular heterogeneity and mechanisms of tumorigenesis at the single cell level.
An Association Test of the Spatial Distribution of Rare Missense Variants within Protein Structures Improves Statistical Power of Sequencing Studies
Authors: Jin Bowen , Capra John A. , Benchek Penelope , Wheeler Nicholas , Naj Adam C. , Hamilton-Nelson Kara L. , Farrell John J. , Leung Yuk Yee , Kunkle Brian , Vadarajan Badri , Schellenberg Gerard D. , Mayeux Richard , Wang Li-san , Farrer Lindsay A. , Pericak-Vance Margaret A. , Martin Eden R. , Haines Jonathan L. , Crawford Dana C. , Bush William S. 
Published: August 2021

ABSTRACTOver 90% of variants are rare, and 50% of them are singletons in the Alzheimer’s Disease Sequencing Project Whole Exome Sequencing (ADSP WES) data. However, either single variant tests or unit-based tests are limited in the statistical power to detect the association between rare variants and phenotypes. To best utilize rare variants and investigate their biological effect, we exam their association with phenotypes in the context of protein. We developed a protein structure-based approach, POKEMON (Protein Optimized Kernel Evaluation of Missense Nucleotides), which evaluates rare missense variants based on their spatial distribution on the protein rather than allele frequency. The hypothesis behind this is that the three-dimensional spatial distribution of variants within a protein structure provides functional context and improves the power of association tests. POKEMON identified four candidate genes from the ADSP WES data, namely two known Alzheimer’s disease (AD) genes (TREM2 and SORL) and two novel genes (DUSP18 and CSF1R). For known AD genes, the signal from the spatial cluster is stable even if we exclude known AD risk variants, indicating the presence of additional low frequency risk variants within these genes. DUSP18 has a cluster of variants primarily shared by case subjects around the ligand-binding domain, and this cluster is further validated in a replication dataset with a larger sample size. POKEMON is an open-source tool available at https://github.com/bushlab-genomics/POKEMON.
In-field capable loop-mediated isothermal amplification detection of fall army worm (Spodoptera frugiperda; Lepidoptera: Noctuidae) larvae using a rapid and simple crude extraction technique
Authors: Congdon B. S. , Webster C.G. , Severtson D. , Spafford H. 
Published: August 2021

AbstractFall armyworm,Spodoptera frugiperda(Lepidoptera: Noctuidae), is an economically important pest worldwide and has recently been identified in Australia. Morphological identification ofS. frugiperdaat early larval stages can be difficult often requiring expert microscopy analysis. Rapid and accurate in-field diagnosis is vital for management decision support and there are no tools currently available for this purpose. In this study, a sensitive, specific and in-field capable loop-mediated isothermal amplification (LAMP) assay was developed to detectS. frugiperdalarvae. A primer set based on a highly conserved region of theS. frugiperdacytochrome oxidase subunit 1 (COX1) gene provided detection within 30 min from both total DNA and crude extractions. The crude extraction technique of crushing 10 mg ofS. frugiperdamaterial in 50 μL ddH20 and further diluting the homogenate in ddH20 is rapid, simple and does not require heat blocks, centrifuges or special buffers increasing its utility as a field-based technique. The primer set detected as little as 24 pg ofS. frugiperdaDNA and did not cross-react with any other of the lepidopteran species tested that are easily confused withS. frugiperdain Australia. Therefore, this assay could be used in-field to correctly identify the presence ofS. frugiperdaand thereby greatly assist with timely management decisions.
Fingolimod Regulates BDNF-AS and HOTAIR Expression in Multiple Sclerosis Patients
Authors: Khani-Habibabadi Fatemeh , Sahraian Mohammad Ali , Javan Mohammad , Behmanesh Mehrdad 
Published: August 2021

AbstractBrain-derived neurotrophic factor (BDNF), a member of the neurotrophin family, is expressed by neurons and glial cells in the central nervous system (CNS). In the CNS, BDNF is responsible for neuroprotection and neurogenesis. Recent studies showed that the Fingolimod, the first oral medicine for relapsing-remitting multiple sclerosis (RR-MS), induces BDNF expression. Besides, It is well demonstrated that long noncoding RNAs (lncRNAs) have a pivotal role in gene regulation. This study is mainly focused on how Fingolimod treatment plays role in BDNF regulation in coordination with lncRNAs. An in-silico study was performed to predict BDNF-regulatory candidate lncRNAs using online tools. Then, the expression of BDNF-related lncRNAs was analyzed in patients with relapsing-remitting multiple sclerosis (RRMS) at baseline and after three months of Fingolimod treatment. Based on in silico results, two lncRNAs with potential regulatory functions on the BDNF including, Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) and HOX Transcript Antisense RNA (HOTAIR), and also natural antisense of BDNF were selected. Fingolimod treatment increased the expression of HOTAIR lncRNA; however, the BDNF antisense RNA (BDNF-AS) expression was reduced dramatically. Furthermore, the results indicate a positive correlation between HOTAIR and MALAT1 lncRNAs and BDNF. Also, after Fingolimod treatment, the patients’ EDSS scores were declined or remained unchanged, indicating disease hindrance by Fingolimod therapy. Altogether, fingolimod exerts protective roles in RRMS patients probably by the mediation of HOTIAR and BDNF-AS lncRNAs.
Synergism vs Additivity - Defining the Interactions between Common Disinfectants
Authors: Noel Daniel J. , Keevil C. William , Wilks Sandra A. 
Published: August 2021

ABSTRACTMany of the most common disinfectant and sanitizer products are formulations of multiple antimicrobial compounds. Products claiming to contain synergistic formulations are common, although there is often little supporting evidence. The antimicrobial interactions of all pairwise combinations of common disinfectants (benzalkonium chloride, didecyldimethylammonium chloride, polyhexamethylene biguanide, chlorocresol and bronopol) were classified via checkerboard and validated by time-kill analyses. Combinations were tested againstAcinetobacter baumanniiNCTC 12156,Enterococcus faecalisNCTC 13379,Klebsiella pneumoniaeNCTC 13443 andStaphylococcus aureusNCTC 13143. Synergistic interactions were only identified between cholorocresol with benzalkonium chloride, and chlorocresol with polyhexamethylene biguanide. Synergism was not ubiquitously demonstrated against all species tested and was on the borderline of the synergism threshold. These data demonstrate that synergism between disinfectants is uncommon and circumstantial. Most of the antimicrobial interactions tested were characterised as additive. We suggest that this is due to the broad, non-specific mechanisms associated with disinfectants not providing opportunity for the combined activities of these compounds to exceed the sum of their parts.IMPORTANCEThe scarcity of observed synergistic interactions suggests that many disinfectant-based products may be misinterpreting combined mechanisms of interaction. We emphasise the need to correctly differentiate between additivity and synergism in antimicrobial formulations, as inappropriate classification may lead to unnecessary issues in the event of regulatory changes. Furthermore, we question the need to focus on synergism and disregard additivity when considering combinations of disinfectants, as the benefits that synergistic interactions provide are not necessarily relevant to the application of the final product.
Lessons learned from implementation of interferon-gamma release assay to screen for latent tuberculosis infection in a large multicenter observational cohort study in Brazil
Authors: Costa Allyson G. , Carvalho Brenda K.S. , Araújo-Pereira Mariana , Ibiapina Hiochelson N.S. , Spener-Gomes Renata , Souza Alexandra B. , Gomes-Silva Adriano , Andrade Alice M.S. , Silva Elisangela C. , Arriaga María B. , Benjamin Aline , Rocha Michael S. , Moreira Adriana S.R. , Oliveira Jamile G. , Figueiredo Marina C. , Turner Megan M. , Durovni Betina , Cavalcante Solange , Kritski Afranio L. , Rolla Valeria C. , Sterling Timothy R. , Andrade Bruno B. , Cordeiro-Santos Marcelo ,   the RePORT Brazil Consortium
Published: August 2021

AbstractBackgroundInterferon-gamma release assay (IGRA) has emerged as a useful tool in identifying latent tuberculosis infection (LTBI). This assay can be performed through testing platforms, such as QuantiFERON-TB Gold Plus (QFT®-Plus). This in vitro test has been incorporated by several guidelines worldwide and has recently been considered for the diagnosis of LTBI by the World Health Organization (WHO). The possibility of systematically implementing IGRAs such as QFT®-Plus in centers that perform LTBI screening has been accelerated by the decreased availability of tuberculin skin testing (TST) in several countries. Nevertheless, the process to implement IGRA testing in routine clinical care has many gaps.MethodsThe study utilized the expertise acquired by the laboratory teams of the Regional Prospective Observational Research in Tuberculosis (RePORT)-Brazil consortium during study protocol implementation of LTBI screening of TB close contacts.ResultsRePORT-Brazil includes clinical research sites from Brazilian cities and is the largest multicenter cohort of TB close contacts to date in the country. Operational and logistical challenges faced during IGRA implementation in all four study laboratories are described, as well as the solutions that were developed and led to the successful establishment of IGRA testing in RePORT-Brazil.ConclusionsThe problems identified and resolved in this study can assist laboratories implementing IGRAs, in addition to manufacturers of IGRAs providing effective technical support. This will facilitate the implementation of IGRA testing in countries with a high TB burden, such as Brazil.ImportanceThe interferon-gamma release assay (IGRA) has emerged as a useful tool in identifying persons with latent tuberculosis infection (LTBI). Although the implementation of IGRAs is of utmost importance, to our knowledge, there is scarce information on identification of logistical and technical challenges of systematic screening of for LTBI on a large scale. Thus, the problems identified and resolved in this study can assist laboratories implementing IGRAs, in addition to manufacturers of IGRAs providing effective technical support. This will facilitate the implementation of IGRA testing in countries with a high TB burden, such as Brazil.
Emotions, moods and hyperreality: social media and the stock market during the first phase of COVID-19 pandemic
Authors: Lazzini Arianna , Lazzini Simone , Balluchi Federica , Mazza Marco 
Published: August 2021

PurposeThis paper aims to expand the emerging literature on COVID-19 and the financial markets by searching for a relationship between the uncertainty of the first phase of the COVID-19 pandemic experienced through social media and the extreme volatility of the Italian stock market.Design/methodology/approachThe authors analyze the relationship between social media and stock market trends during the first phase of the COVID-19 pandemic through the lens of social theory and Baudrillard's simulacra and hyperreality theory. The authors conducted the data analysis in two phases: the emotional and Granger correlation analysis by using the KPI6 software to analyze 3,275,588 tweets for the predominant emotion on each day and observe its relationship with the stock market.FindingsThe research results show a significant Granger causality relation between tweets on a particular day and the closing price of the FTSE MIB during the first phase of the COVID-19 epidemic. The results highlight a strong relationship between social media hyperreality and the real world. The study confirms the role of social media in predicting stock market volatility.Research limitations/implicationsThe findings have theoretical and practical implications as they reveal the relevance of social media in our society and its relationship with businesses and economies. In an emergency, social media, as an expression of users' feelings and emotions, can generate a state of hyperreality that is strong correlated with reality. Since social media allows users to publish and share messages without any filter and mediation, the hyperreality generated is affected by highly subjective elements.Originality/valueThis research is different from the previous ones on the same topic because unlike previous studies, conducted under normal or simulated scenarios, this study is focused on the first phase of an unpredictable and unforeseen emergency event: the COVID-19 pandemic. This research adopts a multidisciplinary approach and integrates previous studies on the economic and financial effects generated by social media by applying well-known theories to a new and unexplored context. The study reveals the significant impact generated by social media on stock markets during a global pandemic.
“It’s selling like hotcakes”: deconstructing social media influencer marketing in long-form video content on youtube via social influence heuristics
Authors: Rohde Paul , Mau Gunnar 
Published: August 2021

PurposeThis study aims to examine the ability of the social influence heuristics framework to capture skillful and creative social media influencer (SMI) marketing in long-form video content on YouTube for influencer-owned brands and products.Design/methodology/approachThe theoretical lens was a framework of seven evidence-based social influence heuristics (reciprocity, social proof, consistency, scarcity, liking, authority and unity). For the methodological lens, a qualitative case study approach was applied to a purposeful sample of 6 SMIs and 15 videos on YouTube.FindingsThe evidence shows that self-promotional influencer marketing in long-form video content is relatable to all seven heuristics and shows signs of high elaboration, innovativeness and skillfulness.Research limitations/implicationsThe study reveals that a heuristic-based account of self-promotional influencer marketing in long-form video content can greatly contribute to the understanding of how various well-established marketing concepts (e.g. source attractivity) might be expressed in real-world communications and behaviors. Based on this improved, in-depth understanding, current research efforts, such as experimental studies using one video with a more or less arbitrary influencer and pre-post measure, are advised to explore research questions via designs that account for the observed subtle and complex nature of real-world influencer marketing in long-form video content.Practical implicationsThis structured account of skillful and creative marketing can be used as educational and instructive material for influencer marketing practitioners to enhance their creativity, for consumers to increase their marketing literacy and for policymakers to rethink policies for influencer marketing.Originality/valuePrior research has created a body of knowledge on influencer marketing. However, a conceptual disconnect has hampered the advancement of the field. The social influence heuristics framework is a highly functional conceptual bridge that links the qualitative and quantitative evidence and will advance the understanding of influencer marketing more effectively.
Supply chain integration and export performance: the mediating role of supply chain performance
Authors: Abdallah Ayman Bahjat , Rawadiah Omar Mohammad , Al-Byati Walaa , Alhyari Salah 
Published: August 2021

PurposeThe purpose of this study is to examine the effect of supply chain integration (SCI) in terms of supplier, customer and internal integration on supply chain performance (SCP) and export performance (EXP). The effect of SCP on EXP is also explored. This study further seeks to examine the mediating effect of SCP on the relationship between the types of SCI and EXP.Design/methodology/approachThe population of this study consists of manufacturing companies in different industries in Jordan. Data were gathered using self-administered questionnaires; managers from 271 companies responded to the survey. The study constructs were assessed for validity and reliability, and it was ensured that acceptable levels of these tests were obtained. Structural equation modeling (SEM) was used to test the study hypotheses.FindingsThe findings showed that supplier and customer integration were not drivers of EXP, but internal integration positively impacted EXP. In addition, internal and customer integration positively affected SCP, while supplier integration did not. Also, SCP positively impacted EXP. Furthermore, customer integration and internal integration indirectly impacted EXP through SCP.Practical implicationsManufacturers should establish both intra- and inter-organizational collaborations to improve their performance. Specifically, managers in developing countries need to pay substantial attention to internal integration, as it is the key antecedent of both SCP and EXP. Furthermore, managers must be aware of the essential role of customer integration in improving SCP and subsequently EXP. Therefore, they should make long-term plans to integrate and incorporate key customers. In addition, managers are advised to reconsider their current relationships with suppliers. By failing to take advantage of the valuable expected contribution of supplier integration, manufacturers may lose export opportunities to international competitors.Originality/valueThe present study addresses an evident gap in the available literature regarding the effect of SCI on EXP. It tests a comprehensive model underlining the role of SCP on the relationship between SCI types and EXP. This study is also valuable because it was conducted in a developing country. Generally, manufacturing companies in developing countries face more SC-related difficulties than those in developed countries; these challenges can limit the export abilities of manufacturers in developing countries. The study offers important implications for the managers of manufacturing companies to improve their SCP and, subsequently enhance their EXP.
Circular economy indicators and levels of innovation: an innovative systematic literature review
Authors: Kuzma Edson Luis , Sehnem Simone , Lopes de Sousa Jabbour Ana Beatriz , Campos Lucila M.S. 
Published: August 2021

PurposeThis article aims to analyze the specific indicators of the circular economy (CE) in terms of analytical aspects, scope and breadth of metrics and levels of innovation associated with CE.Design/methodology/approachA literature review was developed with a sample of 125 articles, extracted from Scopus, Web of Science, ScienceDirect, Emerald, Google Scholar, Online Library, Sage, Springer, Taylor and Francis and JSTOR databases.FindingsThe results indicate the lack of integration of the social dimension and predominance of environmental indicators, lack of indicators for the meso level and concentration of metrics for the product level. Methodological criteria of validity and reliability for measurement studies are recommended, as well as paths and proposals for future research in the CE.Research limitations/implicationsThe study’s limitations are linked to the content and method aspects. Although the search was performed in several databases, with a significant number of articles returned compared to other reviews of the topic, the possibilities are limited by the data source and the impossibility of a broader review. The theme is not yet consolidated and this affects the linearity of the revised results. As for the method, the analysis and coding in systematic reviews involve the authors’ capacity for exploration and cognition.Practical implicationsThe article proposes six theoretical propositions and the theoretical framework that portrays the main findings of the study and questions to drive future research in the topic.Social implicationsThe article points out opportunities for companies, universities and the government regarding the possibilities that can be explored to develop knowledge and practice about the field.Originality/valueThis research advances the CE literature by means of providing a review of the indicators, metrics and tools oriented toward the CE literature that contributes to the improvement and consolidation of the various researches in the field.
Discourses of fact-checking in Swedish news media
Authors: Juneström Amalia 
Published: August 2021

PurposeThe purpose of this paper is to examine how contemporary fact-checking is discursively constructed in Swedish news media; this serves to gain insight into how this practice is understood in society.Design/methodology/approachA selection of texts on the topic of fact-checking published by two of Sweden’s largest morning newspapers is analyzed through the lens of Fairclough’s discourse theoretical framework.FindingsThree key discourses of fact-checking were identified, each of which included multiple sub-discourses. First, a discourse that has been labeled as “the affirmative discourse,” representing fact-checking as something positive, was identified. This discourse embraces ideas about fact-checking as something that, for example, strengthens democracy. Second, a contrasting discourse that has been labeled “the adverse discourse” was identified. This discourse represents fact-checking as something precarious that, for example, poses a risk to democracy. Third, a discourse labeled “the agency discourse” was identified. This discourse conveys ideas on whose responsibility it is to conduct fact-checking.Originality/valueA better understanding of the discursive construction of fact-checking provides insights into social practices pertaining to it and the expectations of its role in contemporary society. The results are relevant for journalists and professionals who engage in fact-checking and for others who have a particular interest in fact-checking, e.g. librarians and educators engaged in media and information literacy projects.