bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins
Authors: Narayanan Krishna K. , Amaya Moushimi , Tsang Natalie , Yin Randy , Jays Alka , Broder Christopher C. , Shukla Diwakar , Procko Erik 
Published: April 2023

ABSTRACTEphrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and functions as a cell entry receptor for several henipaviruses including Nipah virus (NiV), a pathogenic zoonotic virus with pandemic potential. To understand the sequence basis of promiscuity for EFNB2 binding to the attachment glycoprotein of NiV (NiV-G) and Eph receptors, we performed deep mutagenesis on EFNB2 to identify mutations that enhance binding to NiV-G over EphB2, one of the highest affinity Eph receptors. The mutations highlight how different EFNB2 conformations are selected by NiV-G versus EphB2. Specificity mutations are enriched at the base of the G-H binding loop of EFNB2, especially surrounding a phenylalanine hinge upon which the G-H loop pivots, and at a phenylalanine hook that rotates away from the EFNB2 core to engage Eph receptors. One EFNB2 mutant, D62Q, possesses pan-specificity to the attachment glycoproteins of closely related henipaviruses and has markedly diminished binding to the six Eph receptors. However, EFNB2-D62Q has high residual binding to EphB3 and EphB4. A second deep mutational scan of EFNB2 identified combinatorial mutations to further enhance specificity to NiV-G. A triple mutant of soluble EFNB2, D62Q-Q130L-V167L, has minimal binding to Eph receptors but maintains binding, albeit reduced, to NiV-G. Soluble EFNB2 decoy receptors carrying the specificity mutations were potent neutralizers of chimeric henipaviruses. These findings demonstrate how specific residue changes at the shared binding interface of a promiscuous ligand (EFNB2) can influence selectivity for multiple receptors, and may also offer insight towards the development of henipavirus therapeutics and diagnostics.IMPORTANCEEphrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and regulates multiple cell developmental and signaling processes. It also functions as the cell entry receptor for Nipah virus and Hendra virus, zoonotic viruses that can cause respiratory and/or neurological symptoms in humans with high mortality. Here, we investigate the sequence basis of EFNB2 specificity for binding the Nipah virus attachment G glycoprotein over Eph receptors. We then use this information to engineer EFNB2 as a soluble decoy receptor that specifically binds the attachment glycoproteins of Nipah virus and other related henipaviruses to neutralize infection. These findings further mechanistic understanding of protein selectivity and may facilitate the development of diagnostics or therapeutics against henipavirus infection.
Quantifying cell viability through organelle ratiometric probing
Authors: Chen Rui , Qiu Kangqiang , Han Guanqun , Kundu Bidyut Kumar , Ding Guodong , Sun Yujie , Diao Jiajie 
Published: April 2023

AbstractDetecting cell viability is crucial in research involving the precancerous discovery of abnormal cells, the evaluation of treatments, and drug toxicity testing. Although conventional methods afford cumulative results regarding cell viability based on a great number of cells, they do not permit investigating cell viability at the single-cell level. In response, we rationally designed and synthesized a fluorescent probe, PCV-1, to visualize cell viability under the super-resolution technology of structured illumination microscopy. Given its sensitivity to mitochondrial membrane potential and affinity to DNA, PCV-1’s ability to stain mitochondria and nucleoli was observed in live and dead cells, respectively. During cell injury induced by drug treatment, PCV-1’s migration from mitochondria to the nucleolus was dynamically visualized at the single-cell level. By extension, harnessing PCV-1’s excellent photostability and signal-to-noise ratio and by comparing the fluorescence intensity of the two organelles, mitochondria and nucleoli, we developed a powerful analytical assay namedorganelle ratiometric probing(ORP) that we applied to quantitatively analyze and efficiently assess the viability of individual cells, thereby enabling deeper insights into the potential mechanisms of cell death. In ORP analysis with PCV-1, we identified 0.3 as the cutoff point for assessing whether adding a given drug will cause apparent cytotoxicity, which greatly expands the probe’s applicability. To the best of our knowledge, PCV-1 is the first probe to allow visualizing cell death and cell injury under super-resolution imaging, and our proposed analytical assay using it paves the way for quantifying cell viability at the single-cell level.
A Rapid Inducible RNA Decay system reveals fast mRNA decay in P-bodies
Authors: Blake Lauren A. , Liu Yang , Inoue Takanari , Wu Bin 
Published: April 2023

AbstractRNA decay plays a crucial role in regulating mRNA abundance and gene expression. Modulation of RNA degradation is imperative to investigate an RNA’s function. However, information regarding where and how RNA decay occurs remains scarce, partially because existing technologies fail to initiate RNA decay with the spatiotemporal precision or transcript specificity required to capture this stochastic and transient process. Here, we devised a general method that employs inducible tethering of regulatory protein factors to target RNAs and modulate their metabolism. Specifically, we established a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNA within minutes. The fast and synchronous induction enabled direct visualization of mRNA decay dynamics in cells with spatiotemporal precision previously unattainable. When applying RIDR to endogenousACTBmRNA, we observed rapid formation and disappearance of RNA granules, which coincided with pre-existing processing bodies (P-bodies). We measured the time-resolved RNA distribution in P-bodies and cytoplasm after induction, and compared different models of P-body function. We determined that mRNAs rapidly decayed in P-bodies upon induction. Additionally, we validated the functional role of P-bodies by knocking down specific a P-body constituent protein and RNA degradation enzyme. This study determined compartmentalized RNA decay kinetics for the first time. Together, RIDR provides a valuable and generalizable tool to study the spatial and temporal RNA metabolism in cells.
Arbitrium communication controls phage life-cycle through modulation of a bacterial anti-phage defense system
Authors: Guler Polina , Omer Bendori Shira , Aframian Nitzan , Kessel Amit , Eldar Avigdor 
Published: April 2023

AbstractBacterial temperate viruses (phages) have to decide between a quiescent (lysogenic) and virulent (lytic) lifestyle in the face of a variety of phage defense systems. MultipleBacilliphage families have been shown to use the arbitrium communication system, but the mechanism by which the arbitrium system exerts its function remains largely unknown. Here we study phage ɸ3T, in which arbitrium was originally identified, and find that arbitrium communication controls the phage life-cycle through interactions with a host-encoded defense system. Under lytic conditions, the arbitrium system expresses an anti-toxin, AimX, which blocks the RNA ribonuclease activity of MazF, part of the MazEF toxin-antitoxin system. When arbitrium signal concentration is high, AimX is not expressed and MazF remains active. We find that this activity is necessary for lysogenization. Finally, we show that MazEF acts as a defense system, and protects bacteria against a lytic ɸ3T mutant which lacks AimX and an additional later-expressed MazE-like antitoxin, YosL. Altogether, our results show how a bacterial defense system has been co-opted by phages to control their lysis/lysogeny decision-making.
Live-cell super-resolution nanoscopy reveals modulation of cristae dynamics in bioenergetically compromised mitochondria
Authors: Golombek Mathias , Tsigaras Thanos , Schaumkessel Yulia , Hänsch Sebastian , Weidtkamp-Peters Stefanie , Anand Ruchika , Reichert Andreas S. , Kondadi Arun Kumar 
Published: April 2023

AbstractCristae membranes have been recently shown to undergo intramitochondrial merging and splitting events. Yet, the metabolic and bioenergetic factors regulating them are unclear. Here we investigated whether and how cristae membrane remodelling is dependent on oxidative phosphorylation (OXPHOS) complexes, the mitochondrial membrane potential (ΔΨm), and the ADP/ATP nucleotide translocator. Advanced live-cell STED nanoscopy combined with in-depth quantification were employed to analyse cristae morphology and dynamics after treatment of mammalian cells with rotenone, antimycin A, oligomycin A and CCCP. This led to formation of enlarged mitochondria along with reduced cristae density but did not change the number of cristae remodelling events. CCCP treatment leading to ΔΨmabrogation even enhanced the cristae dynamics showing their ΔΨm-independent nature. Inhibition of OXPHOS complexes was accompanied by reduced ATP levels but did not affect cristae dynamics. However, inhibition of ADP/ATP exchange led to aberrant cristae morphology and impaired cristae dynamics in a mitochondrial subset. In sum, we provide quantitative data of cristae membrane remodelling under different conditions supporting an important interplay between OXPHOS, metabolite exchange and cristae membrane dynamics.Summary BlurbCristae morphology and dynamics are intricately connected
Dynamics and Plasticity of Immune Cells within Tumor Microenvironment
Authors: Wei Chuijin , Dong Liaoliao , Xiong Shumin , Yu Ping , Zhou Ren , Cheng Lin 
Published: April 2023

AbstractExtensive research has been conducted on the heterogenicity of immune cells within the tumor microenvironment, like cancer cell heterogenicity, particularly with the emergence of single cell analysis. While inducing factors have been used to artificially alter immune cell fatein vitroand dynamic cancer cell plasticity has been recently discovered, it remains unknown whether tumor infiltrating immune cells acquire plasticity and dynamics that contribute to heterogenicity. In this study, we explored mitochondrial DNA mutation combining with chromosome single nucleotide polymorphism to construct phylogenetic trees of immune cells within multiple solid tumors, together with precise cell type and subtype definition based on single cell RNA sequencing data. Based on these lineage tracing landscapes, we systematically identified cell state transitions and fate changes among different immune cell subtypes and types within multiple solid tumors. Interestingly, immune cells demonstrated a high level of plasticity for transitioning between different states, transdifferentiating from one type to another or dedifferentiating to a progenitor stage, in varying frequencies across different cancers. Moreover, most of these cell state transitions and cell fate changes discovered here were previously unknown. The cell changes may arise from extrinsic growth factors and cytokines secreted by tumor microenvironment cells, but intrinsic genetic mutations, particularly those related to ribosomes, may also be involved. Our data reveal that immune cell complexity extends beyond heterogenicity and also encompasses plasticity similar to that of cancer cells. Understanding the underlying mechanism of these cell changes will help elucidate the role of immune cells in cancer development and manipulating the cell change direction may ultimately enhance the efficiency of current immunotherapy.
Integrating indigenous knowledge and state-of-the-art Earth observation solutions for the Sendai framework implementation
Authors: Pimprikar Milind , Cunningham Myrna , Ravan Shirish , Lambert Simon 
Published: April 2023

PurposeIndigenous peoples represent one of the most vulnerable groups and need access as well as hands-on experience in the use of emerging Earth observations (EO)-based DRR solutions at the community level, while balancing this learning with traditional indigenous knowledge (IK). However, complicating any engagement between EO and IK is the reality that IKs are diverse and dynamic, with location-specific relevance and accuracy. Additionally, the COVID-19 pandemic caused complex risks and cascading effects for which the world was not prepared. Thus, there is a need to examine the lessons learned and motivate emerging EO-based innovations and demonstrations related to DRR and climate change adaptation.Design/methodology/approachHence, this study aims to undertake an in-depth assessment of IK related to DRR covering relevant UN instruments and provides state-of-the-art of opportunities presented by EO-based tools and solutions.FindingsThe overall research strategy was designed to integrate key components of IK for DRR in a coherent and logical way, with those offered by the EO technology developers and providers. There are several EO tools accessible that are relevant to integrate IK and complement DRR. The study examined and identified challenges and barriers to implement workable and replicable EO solutions in pursuit of resilience.Originality/valueThe key findings of this study will help create a balanced approach by acknowledging the importance of IK for DRR with co-development, co-creation and use of culturally relevant EO data and tools for sustainable innovation, capacity building and youth empowerment. The technological inequalities appear to be growing, and it would be challenging to meet the Sendai Framework indicators.
A group recommender system for books based on fine-grained classification of comments
Authors: Ye Jiaxin , Xiong Huixiang , Guo Jinpeng , Meng Xuan 
Published: April 2023

PurposeThe purpose of this study is to investigate how book group recommendations can be used as a meaningful way to suggest suitable books to users, given the increasing number of individuals engaging in sharing and discussing books on the web.Design/methodology/approachThe authors propose reviews fine-grained classification (CFGC) and its related models such as CFGC1 for book group recommendation. These models can categorize reviews successively by function and role. Constructing the BERT-BiLSTM model to classify the reviews by function. The frequency characteristics of the reviews are mined by word frequency analysis, and the relationship between reviews and total book score is mined by correlation analysis. Then, the reviews are classified into three roles: celebrity, general and passerby. Finally, the authors can form user groups, mine group features and combine group features with book fine-grained ratings to make book group recommendations.FindingsOverall, the best recommendations are made by Synopsis comments, with the accuracy, recall, F-value and Hellinger distance of 52.9%, 60.0%, 56.3% and 0.163, respectively. The F1 index of the recommendations based on the author and the writing comments is improved by 2.5% and 0.4%, respectively, compared to the Synopsis comments.Originality/valuePrevious studies on book recommendation often recommend relevant books for users by mining the similarity between books, so the set of book recommendations recommended to users, especially to groups, always focuses on the few types. The proposed method can effectively ensure the diversity of recommendations by mining users’ tendency to different review attributes of books and recommending books for the groups. In addition, this study also investigates which types of reviews should be used to make book recommendations when targeting groups with specific tendencies.
Developing public managers' reflective thinking through continuing management education
Authors: Thomassen Anja Overggaard 
Published: April 2023

PurposeThe aim of this paper is to outline how public managers' reflective thinking capacity is developed through integration of education and practice using a real-life organizational problem as the educational starting point. Managers' reflective thinking capacity becomes important due to an increasing organizational complexity and the growing trend of introducing post-new public management paradigms.Design/methodology/approachInspired by Brinkmann's (2012) approach to the inquiry on everyday life materials, semi-structured interviews were conducted with public managers taking a public management program. A phenomenologically inspired content analysis was applied in the process of scrutinizing the findings, subsequently informing the discussion on the development of problem solving through public management education.FindingsThe analysis indicates that the managers' pre-understanding of continuing education at the university level, managers' personal objectives, along with a growing experience with and insights into problem-based learning (PBL), appear to facilitate managers' integration of theory and practice. As revealed in this paper, an inquiry that integrates daily organizational practice and theoretical models and terms, as the origin of the personal development module, seems to facilitate managers' reflective thinking and self-reflexivity.Originality/valueThis paper illustrates that learning processes facilitated by seminars like the personal development module (PDM) not only facilitates the development of reflective thinking, but managers also seem to develop competencies in self-reflexivity – the latter being an underdeveloped element of Dewey's (1933) notion of reflective thinking. Thus, further theoretical and empirical research is needed to explore the potentials of developing a pragmatically inspired notion that offers an understanding of managers' self-reflexivity. By inquiring about managerial puzzlements through a personal development lens, a self-reflective focus adds to the Dewey-inspired approach to reflective thinking.
Probability estimation in accounting: subjective numeracy matters
Authors: Zhang Yuqian , Seufert Juergen , Dellaportas Steven 
Published: April 2023

PurposeThis study examined subjective numeracy and its relationship with accounting judgements on probability issues.Design/methodology/approachA subjective numeracy scale (SNS) questionnaire was distributed to 231 accounting students to measure self-evaluated numeracy. Modified Bayesian reasoning tasks were applied in an accounting-related probability estimation, manipulating presentation formats.FindingsThe study revealed a positive relationship between self-evaluated numeracy and performance in accounting probability estimation. The findings suggest that switching the format of probability expressions from percentages to frequencies can improve the performance of participants with low self-evaluated numeracy.Research limitations/implicationsAdding objective numeracy measurements could enhance results. Future numeracy research could add objective numeracy items and assess whether this influences participants' self-perceived numeracy. Based on this sample population of accounting students, the findings may not apply to large populations of accounting-information users.Practical implicationsInvestors' ability to exercise sound judgement depends on the accuracy of their probability estimations. Manipulating the format of probability expressions can improve probability estimation performance in investors with low self-evaluated numeracy.Originality/valueThis study identified a significant performance gap among participants in performing accounting probability estimations: those with high self-evaluated numeracy performed better than those with low self-evaluated numeracy. The authors also explored a method other than additional training to improve participants' performance on probability estimation tasks and discovered that frequency formats enhanced the performance of participants with low self-evaluated numeracy.
Investor attention and IPO returns: evidence from Indian markets
Authors: Mulchandani Poonam , Pandey Rajan , Debata Byomakesh , Renganathan Jayashree 
Published: April 2023

PurposeThe regulatory design of Indian stock market provides us with the opportunity to disaggregate initial returns into two categories, i.e. voluntary premarket underpricing and post market mispricing. This study explores the impact of investor attention on the disaggregated short-run returns and long-run performance of initial public offerings (IPOs).Design/methodology/approachThe study employs regression techniques on the sample of IPOs listed from 2005 to 2019. It measures investor attention with the help of the Google Search Volume Index (GSVI) extracted from Google Trends. Along with GSVI, the subscription rate is used as a proxy to measure investor attention.FindingsThe empirical results suggest a positive and significant relationship between initial returns and investor attention, thus validating the attention theory for Indian IPOs. Furthermore, when the returns are analysed for a more extended period using buy-and-hold abnormal returns (BHARs), it was found that price reversal holds in the long run.Research limitations/implicationsThis study highlights the importance of information diffusion in the market. It emphasizes the behavioural tendency of the investors in the pre-market, which reduces the market efficiency. Hence, along with fundamentals, investor attention also plays an essential role in deciding the returns for an IPO.Originality/valueAccording to the best of the authors’ knowledge, this is one of the first studies that has attempted to explore the influence of investor attention and its interplay with underpricing and long-run performance for IPOs of Indian markets.
Dynamic relationship of volatility of returns across different markets: evidence from selected next 11 countries
Authors: Shafiq Sadia , Qureshi Saiqa Saddiqa , Akbar Muhammad 
Published: April 2023

PurposeThis paper aims to examine whether the volatility of returns in commodity (gold, oil), bond and forex markets is related over time to the volatility of returns in equity markets of Bangladesh, Indonesia, Pakistan, Philippines, Turkey and Vietnam. In addition, the authors analyze the integration of the commodity, bond, forex and equity markets across these markets.Design/methodology/approachThe dynamic conditional correlation GARCH (DCC-GARCH) model is used to capture the time-varying conditional correlation among markets. The authors use daily data of stock prices, oil prices, gold prices, exchange rates and 10 years' bond yields of the six countries from Datastream and investing.com from January 2001 to April 2021.FindingsFindings reveal that the parameters of dynamic correlation are statistically significant which indicates the importance of time-varying co-movements. Estimation of the DCC-GARCH model suggests that the stock market is significantly correlated with bond, forex, gold and oil markets in all six countries.Practical implicationsThis study has practical implications for policymakers and investment professionals. A better understanding of dynamic linkages among the markets would help in constructing effective hedging and portfolio diversification strategies. Policy makers can get insight to build proper strategies in order to insulate the economy from factors that cause volatility.Originality/valueSeveral studies have investigated the linkage between commodity and stock markets and the volatility spillover effect, but very little attention is given to study the interrelationship between groups of market segments of different economies. No study has comparatively examined the dynamic relationship of multiple markets of a group of emerging countries simultaneously.