bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of extracellular vesicles isolated fromSorghum bicolorreveals a conservation between monocot and eudicot extracellular vesicle proteomes
Authors: Chaya Timothy , Banerjee Aparajita , Rutter Brian D. , Adekanye Deji , Ross Jean , Hu Guobin , Innes Roger W. , Caplan Jeffrey L. 
Published: May 2023

AbstractPlant extracellular vesicles (EVs) are membrane bound organelles involved mainly in intercellular communications and defense responses against pathogens. Recent studies have demonstrated the presence of proteins, nucleic acids including small RNAs, and lipids along with other metabolites in plant EVs. In this paper, we described the isolation and characterization of extracellular vesicles fromSorghum bicolor. Nanoparticle tracking analysis, dynamic light scattering, and cryo-electron tomography showed the presence of a heterogeneous population of EVs isolated from the apoplastic wash of sorghum leaves. Cryo-electron microscopy revealed that EVs had a median size of 110 nm and distinct populations of vesicles with single or multiple lipid bilayers and low or high amounts of contents. The heterogeneity was further supported by data showing that only a subset of EVs that were stained with a membrane dye, Potomac Gold, were also stained with the membrane-permeant esterase-dependent dye, Calcein-acetoxymethyl ester. Proteomic analysis identified 437 proteins that were enriched in multiple EV isolations, with the majority of these also being found in the EV proteome of Arabidopsis. These data suggest a partial conservation of EV contents and function between the monocot, sorghum, and a distantly related eudicot, Arabidopsis.
FUS Facilitates Gene Body Export from Nuclear Condensates
Authors: Lee Seungha Alisa , Uh Emily Gini , Kim Sammantha Sae-Young , Zelko Michael , Kwak Hojoong 
Published: May 2023

ABSTRACTMembraneless nuclear condensates are an emerging model of transcriptional regulation that involves spatially clustered enhancers and genes forming transcription condensates (TCs). We used a physical isolation approach and DNA/nascent RNA analysis to investigate the global organization of the genome in TCs. Comparative analysis of the two revealed the dynamic nature of the genome, with stable localization of promoters, dynamic recruitment of enhancers, and dynamic export of gene bodies out of TCs upon gene activation. Our findings also suggest that the RNA binding protein FUS undergoes decondensation upon nascent RNA binding, facilitating gene body export out of TCs.
Nutlin-3a inducesKRASmutant lung cancer specific methuosis-like cell death that is dependent on GFPT2
Authors: Kim Dasom , Min Dongwha , Kim Joohee , Kim Min Jung , Seo Yerim , Jung Byung Hwa , Kwon Seung-Hae , Lee Ji-Yun 
Published: May 2023

AbstractOncogenicKRASmutation, the most frequent mutation in non-small cell lung cancer (NSCLC), is an aggressiveness risk factor and leads to the metabolic reprogramming of cancer cells by promoting glucose, glutamine, and fatty acid absorption and glycolysis. Lately, sotorasib was approved by the FDA as a first-in-classKRAS-G12C inhibitor. However, sotorasib still has a derivative barrier, which is not effective for otherKRASmutation types, except for G12C. Additionally, resistance to sotorasib is likely to develop, demanding the need for alternative therapeutic strategies. In this study, we found that nutlin-3a, an MDM2 antagonist, inhibited the KRAS-PI3K/Akt-mTOR pathway and disrupted the fusion of both autophagosomes and macropinosomes with lysosomes. This further elucidated non-apoptotic and catastrophic macropinocytosis associated methuosis-like cell death, which was found to be dependent on GFPT2 of the hexosamine biosynthetic pathway, specifically inKRASmutant NSCLC cells. These results indicate the potential of nutlin-3a as an alternative agent for treatingKRASmutant NSCLC cells.
ZIPPI: proteome-scale sequence-based evaluation of protein-protein interaction models
Authors: Zhao Haiqing , Petrey Donald , Murray Diana , Honig Barry 
Published: May 2023

AbstractPredicting protein-protein interactions (PPI) is a challenging problem of central importance in fundamental biology. With the increasing number of available PPI prediction methods and databases, an effective evaluation model would be extremely valuable. Here we introduce ZIPPI (Z-score for Information about Protein-Protein Interfaces), which evaluates structural models of a complex based on sequence co-evolution and conservation involving residues that are in contact in the interface. The interface Z-score (ZIPPI score) is calculated by comparing metrics for interface contacts to metrics obtained from randomly chosen surface residues. Since contacting residues are defined by the structural model, this obviates the need of accounting for indirect interactions with methods such as Direct Coupling Analysis. Although ZIPPI relies on species-paired multiple sequence alignments, its focus on contacting interfacial residues and the avoidance of direct coupling methods makes it computationally efficient. The performance of ZIPPI is evaluated through applications to experimentally determined complexes from the Protein Data Bank (PDB) and to decoys from the Critical Assessment of PRedicted Interactions (CAPRI) experiment. We demonstrate how ZIPPI can be implemented on a genome-wide scale by calculating scores for millions of structural models of protein-protein interactions in theE. coliinteractome as predicted by PrePPI. Many PrePPI predictions filtered by ZIPPI score are novel. In all, this proteome-scale method shows promising feasibility for applications to the full human protein interactome, which is not yet accessible to deep learning methods.
Identification of post-transcriptional modifications in nucleic acid sequences using purpose-designed molecular beacons
Authors: Sahu Parul , Pereira Getulio , Wang Jian , Szeliski Kamil , Dokholyan Nikolay , Tran Vivian , Korneck Miroslaw , Tigges John , Jones Jennifer , Ghiran Ionita 
Published: May 2023

AbstractPost-transcriptional RNA modifications (PTxMs) present in small RNA species, specifically circulating extracellular RNAs, were recently identified as clinically relevant readouts, often more indicative of disease severity than the classical “up and down” changes in their copy number alone. While identification of PTxMs requires multiple and complex sample preparation steps, microgram-range amounts of RNA, followed by expensive and protracted bioinformatics analyses, the clinically relevant information is usually a yes/no for a particular genetic variant(s), and an up/down answer for relevant biomarkers. We have previously shown that molecular beacons (MBs) can identify specific nucleic acid sequences with picomolar sensitivity and single nucleotide specificity by exploiting the target-dependent change in their electrophoretic mobility profile. We now present a method for direct identification of miRNAs and isomiRs in cells and extracellular vesicles using gel electrophoresis, without the need for RNA isolation and purification. The detection is based on discreet changes in the hydrodynamic surface profile, the overall size, charge and charge distribution of the MB-target hybrid. Furthermore, using an RNA tertiary structure prediction algorithm (iFoldRNA) and a custom molecular dynamics simulation (DMD), we designed modified MBs specific for m6A-modified nucleotides in target RNA sequences. The sample preparation method coupled to the software package affords the design of specific MBs and sensitive, multiplex-type detection of targets in a wide variety of biofluids and cells, in a simple mix and read approach.
Multimodal imaging for identifying brain markers of human prosocial behavior
Authors: Ishihara Toru , Tanaka Hiroki , Kiyonari Toko , Matsuda Tetsuya , Takagishi Haruto 
Published: May 2023

AbstractHow is the high degree of prosocial behavior that characterizes humans achieved? Here, we examined the structural and functional basis of the human brain with prosocial behavior using multimodal brain imaging data and 15 economic games. We identified that stronger interhemispheric connectivity, greater corpus callosum volume, higher functional segregation and integration, and fewer myelin maps combined with a thicker cortex were strongly associated with prosocial behavior. These associations were found especially in the social brain regions. This suggests that the strength of functional/structural connectivity between the left and right hemispheres, the strength of modular and efficient networks, and the high number of non-myelinated cells (i.e., dendrites, spines, synapses, and glia) are strongly associated with higher prosocial behavior in humans, particularly in the social brain regions.
Genuine beta bursts in human working memory: controlling for the influence of lower-frequency rhythms
Authors: Rodriguez-Larios Julio , Haegens Saskia 
Published: May 2023

AbstractHuman working memory is associated with significant modulations in oscillatory brain activity. However, the functional role of brain rhythms at different frequencies is still debated. Modulations in the beta frequency range (15–40 Hz) are especially difficult to interpret because they could be artifactually produced by (more prominent) oscillations in lower frequencies that show non-sinusoidal properties. In this study, we investigate beta oscillations during working memory while controlling for the possible influence of lower frequency rhythms. We collected electroencephalography (EEG) data in 31 participants who performed a spatial working-memory task with two levels of cognitive load. In order to rule out the possibility that observed beta activity was affected by non-sinusoidalities of lower frequency rhythms, we developed an algorithm that detects transient beta oscillations that do not coincide with more prominent lower frequency rhythms in time and space. Using this algorithm, we show that the amplitude and duration of beta bursts decrease with memory load and during memory manipulation, while their peak frequency and rate increase. In addition, interindividual differences in performance were significantly associated with beta burst rates. Together, our results show that beta rhythms are functionally modulated during working memory and that these changes cannot be attributed to lower frequency rhythms with non-sinusoidal properties.
Audiovisual stimuli enhance narrowband gamma activity along the mouse thalamocortical visual circuit
Authors: Lemercier Clément E. , Krieger Patrik , Manahan-Vaughan Denise 
Published: May 2023

AbstractTo what extent thalamic activity can contribute to multisensory integration at cortical level is unclear. To explore this aspect, we used the mouse narrowband gamma oscillations (NBG), which arise from the lateral geniculate nucleus (LGN) and from upstream retinal inputs, as a tool to investigate potential thalamic audiovisual information transfer to the primary visual cortex (V1). We found that simultaneous bimodal audiovisual stimulation increased the power of V1 NBG. Pharmacological and optogenetic manipulations demonstrated that V1 NBG audiovisual responses occurred independently of primary auditory cortex activation. LGN recordings revealed that the majority of its neurons exhibited audiovisual properties. These properties comprised an increase of both the visual-evoked response and gamma-rhythmicity, indicating that the modulation of V1 NBG by audiovisual stimuli likely has a thalamic origin. Our results reveal a previously unreported subcortical source of audiovisual information transfer in V1 and suggest a new role for the LGN as a multisensory integration and relay center.
Determinants of students’ satisfaction with digital classroom services: moderating effect of students’ level of study
Authors: Momen Md Abdul , Sultana Seyama , Hoque Md. Anamul , Shahriar Shamsul Huq Bin , Ashif Abu Sadat Muhammad 
Published: May 2023

PurposeLike every other sector, educational institutions have also been suffering immensely due to COVID-19 pandemic. Many educational institutions are now adopting digital classroom services. However, an online platform with the need for appropriate technology and infrastructure from the students’ perspective poses a severe challenge to developing countries like Bangladesh. The paper aims to figure out the relevant factors that affect the extent of student satisfaction with digital classroom services at the school and tertiary levels.Design/methodology/approachIt is a quantitative study of 450 students from Bangladesh who encountered online classes during the pandemic of COVID-19. An equal number of students from all levels, including schools, colleges and tertiary stages, participated in the survey. Exploratory and confirmatory factor analyses are used to interpret the data. Structural equation modeling using AMOS graphic software is incorporated to test the study’s hypothesis.FindingsAmong all the four determinants of student satisfaction during this critical era, all levels look satisfied with the three underlying influences: technological, convenience and resource-related factors. However, school-level students found the digital classroom services abrasive with Internet connectivity and technical structures during online classes and exams.Research limitations/implicationsA comprehensive study can assess the difference between private and public university students in this regard. In addition, the impact of gender and/or location (rural/urban area) can be assessed by using the same model of the study.Practical implicationsHaving the experience of the students’ satisfaction level during this pandemic, the government, educational institutions and other stakeholders can take away the findings of the results to have a better plan for Internet-based education at every level.Originality/valueThe study is unique to see the readiness of developing nations such as Bangladesh to focus on the sudden uncertainty like a pandemic in introducing the digital education platform. The study can add value to achieving the country’s sustainable development goal of becoming a digitally enabled regional education hub.
Scenario analysis and climate change: a literature review via text analytics
Authors: Aversa Dario 
Published: May 2023

PurposeClimate change has a direct impact on companies. Therefore, the scenario analysis is used to provide companies and stakeholders in this specific sector with forward-looking measures and narratives of the world's future state. This work aims to provide an independent, wide and rigorous literature review on the topics of scenario analysis and climate change, analyzing a large set of referred papers included in economic journals on the Web of Science Clarivate Analytics data source. This review, by means of a mixed approach, can help address new policy strategies and business models.Design/methodology/approachThe work employs 416 abstracts and relative titles in the field of economics, employing data mining for qualitative variables and performing descriptive statistics and lexicometric measures, similarity analysis and clustering with Reinert's hierarchical method in order to extract knowledge. Furthermore, qualitative content analysis allows for the return of a comprehensive and complete universe of meaning, as well as the analysis of co-occurences.FindingsContent analysis reveals three main classification clusters and four unknown patterns: model area, risks, emissions and energy and carbon pricing, indicating research directions and limitations through an overview with an extensive reference bibliography. In the research, the prevalent use of quantitative instruments and their limitations emerge, while qualitative instruments are residual for climate change assessment; they also highlight the centrality of transition risk over adaptation measures and the combination of different types of instruments with reference to carbon pricing.Originality/valueScenario analysis is a relatively new topic in economics and finance research, and it is under-investigated by the academy. The analysis combines quantitative and qualitative research using text analytics.
Putting school-based mentors' experience into context: a mixed-methods cross-country comparison
Authors: Bufali Maria Vittoria , Morton Alec , Connelly Graham 
Published: May 2023

PurposeCross-national research on cultural differences can help understand what drives, in differing contexts, mentors' commitment to school-based mentoring programs. This comparative study aims to explore whether adult volunteers, from Scotland and Italy, experience being mentors of vulnerable youth differently.Design/methodology/approachData from interviews (n = 20) and questionnaires (n = 114) were used to test hypotheses concerning volunteer mentors' perceptions of their role and abilities, as well as motives for participation. According to cross-cultural theories, Scottish mentors should be more likely to identify mentoring with establishing friendly relationships with mentees and promoting youth self-empowerment. They should also be more self-confident and value-driven as volunteers.FindingsDespite the mixed support for the assumptions concerning how the mentor role is conceived, Scottish mentors were less likely than Italians to doubt their abilities and more driven by other-focused and generative concerns.Originality/valueThe study reveals significant variations in how volunteers from countries featuring different welfare regimes and cultural orientations experience mentoring. The research advances the understanding of how culturally sensitive approaches can foster mentors' engagement.
Legitimizing the game: how gamers' personal experiences shape the emergence of grassroots collective action in esports
Authors: Cestino Joaquin , Macey Joseph , McCauley Brian 
Published: May 2023

PurposeThis paper studies early stages of actor mobilization for institutional change within Swedish esports.Design/methodology/approachThe authors employ interpretative phenomenological analysis.FindingsThe authors’ findings explain how actors become motivated to act in critical reflections linked to conflicting legitimacy judgments and emotionally charged personal struggles. Moreover, the findings show how, as actors get activated in collective action, they identify efficacy lines around valid domains and experience emotionally charged collective endeavors. Furthermore, the findings explain how particularities in early experiences project legitimacy aspirations that orient collective action toward validity ends and particular values and ideals shaping actors' grassroots movements.Originality/valueThis study adds to legitimacy and institutional change theory through individual actors' perspectives, providing key insights into how they are motivated, activated, and oriented. This study is the first to investigate grassroots activists' personal stories in esports.
The quality assessment of stakeholder engagement disclosure in the EU mandatory non-financial reporting framework
Authors: Petruzzelli Saverio , Badia Francesco 
Published: May 2023

PurposeThis article investigates the quality of stakeholder engagement (SE) process disclosure in the context of non-financial reporting (NFR) introduced by Directive 2014/95/EU (NFRD). SE implies the involvement of the subjects interested in the organization's activity, according to the principle of inclusiveness and the key concepts of the stakeholder theory (ST).Design/methodology/approachThe authors conducted a content analysis on 75 non-financial statements (NFSs) published by companies listed on the Italian Stock Exchange in 2018 and 2021 to evaluate the evolutionary profiles of SE quality through the years.FindingsThe average level of SE is not significantly high. The research showed an overall poor quality of disclosure concerning stakeholders' key expectations and issues to be addressed and answered. Furthermore, a certain variability emerged in the quality of the disclosure between the various reports, and no significant improvements in SE quality were noted from 2018 to 2021.Research limitations/implicationsThe conclusions provide a replicable method for the analysis of SE quality in NFSs and the development of new standpoints in the ongoing debate on the implications of mandatory legislative frameworks for NFR. Content analyses intrinsically present margins of subjectivity. The sample was limited to a subset of NFS from Italy; hence, the results could be country specific.Practical implicationsThis work suggests some possible ways of improvement of SE practices by companies.Originality/valueOriginal assessment model based on eight variables identified from the academic literature and the most common international sustainability reporting standards. These variables were stakeholder identification, stakeholder selection process, degree of involvement, SE approach, dialogue channels, SE results, different points of view and integration of the SE process.
Why are blood centers not celebrating their success in meeting the blood needs of the United States?
Authors: Sutter Dan 
Published: May 2023

PurposeThis paper reviews the evidence presented in the HHS report and challenges its characterization of the state of the market. The recent US Department of Health and Human Services (HHS) report on the blood industry, Adequacy of the National Blood Supply, provides evidence of and acknowledges that the industry has successfully met demand for blood. And yet the tone and takeaway message of the report of the industry is on the verge of collapse.Design/methodology/approachThe approach of this paper is a critical review of the evidence presented in the HHS report as well as other recent analyses of the blood industry.FindingsWhile acknowledging the successful performance of the industry to date, the HHS report offers hypothetical disaster scenarios and a lack of centralized data as the main causes for concern. These criticisms ignore the satisfactory response of the industry to prior disasters and fail to recognize that centralized information is not necessary for the efficient operation of a decentralized industry.Originality/valueThis paper offers a fresh assessment of a report repeating prior forecasts of doom for an industry which to date has very successfully met the United States' demand for blood.