bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineered Protein Nanosheets for the Scale up of Mesenchymal Stem Cell Culture on Bioemulsions
Authors: Bosch-Fortea Minerva , Nadal Clemence , Chrysanthou Alexandra , Marciano Daniele , Kanso Hassan , Nguyen Nam , Gautrot Julien E. 
Published: December 2023

AbstractThe rapid progress in cell therapies and stem cell technologies requires the development of novel bioprocessing and biomanufacturing pipelines able to cope with the scale up of cell manufacturing. In this respect, microdroplet technologies have already revolutionised the field of biotechnologies, but remain ill-suited to the culture of adherent cells. In this report, we describe the engineering of albumins with cell adhesive peptides for the stabilisation of microdroplets enabling the scale up of mesenchymal stem cell (MSC) expansion. We characterise the modified albumins prior to study their self-assembly at liquid-liquid interfaces via interfacial shear rheology, and mechanical strengthening through the formation of crosslinked nanosheets. The biofunctionalisation of these protein nanosheets is then characterised by fluorescence microscopy. In turn, the ability of the resulting bioactive microdroplets to promote rapid cell adhesion and expansion is examined and the extensive deposition of matrix associated with such cultures is characterised. The culture of MSCs is then scaled up 100 fold, first at the surface of fluorinated oil emulsions, then on plant-based emulsions stabilised by engineered protein nanosheets and the phenotype of resulting cells is characterised. The microdroplet culture system presented displays attractive advantages over existing technologies, in terms of simplicity of processing, compatibility with regulatory expectations and costs of production, and offers exciting opportunities for translation to cell manufacturing, for cell therapies and cultivated meat applications.
CytoCellDB: A Resource Database For Classification and Analysis of Extrachromosomal DNA in Cancer
Authors: Fessler Jacob , Ting Stephanie , Yi Hong , Haase Santiago , Chen Jingting , Gulec Saygin , Wang Yue , Smyers Nathan , Goble Kohen , Cannon Danielle , Mehta Aarav , Ford Christina , Brunk Elizabeth 
Published: December 2023

AbstractExtrachromosomal DNA (ecDNA), or double minute chromosomes, are established cytogenetic markers for malignancy and genome instability. More recently, the cancer community has gained a heightened awareness of the roles of ecDNA in cancer proliferation, drug resistance and epigenetic remodeling. A current hindrance to understanding the biological roles of ecDNA is the lack of available cell line model systems with experimental cytogenetic data that confirm ecDNA status. Although several recent landmark studies have identified common cell lines and tumor models with ecDNA, the current sample size limits our ability to detect ecDNA-driven molecular differences due to limitations in power. Increasing the number of model systems known to express ecDNA would provide new avenues for understanding the fundamental underpinnings of ecDNA biology and would unlock a wealth of potential targeting strategies for ecDNA-driven cancers. To bridge this gap, we created CytoCellDB, a resource that provides karyotype annotations and leverages publicly available global cell line data from the Cancer Dependency Map (DepMap) and the Cancer Cell Line Encyclopedia (CCLE). Here, we identify 139 cell lines that express ecDNA, which is a 200% increase from the current sample size. We expanded the total number of cancer cell lines with ecDNA annotations to 577, which is a 400% increase or 31% of cell lines in CCLE/ DepMap. We demonstrate that a strength of CytoCellDB is the ability to interrogate ecDNA, and a compendium of other chromosomal aberrations, in the context of cancer-specific vulnerabilities, drug sensitivities, and molecular data (genomics, transcriptomics, methylation, proteomics). We anticipate that CytoCellDB will advance cytogenomics research and population-scale discoveries related to ecDNA as well as provide insights into strategies and best practices for determining novel therapeutics that overcome ecDNA-driven drug resistance.
Structures of kinetic intermediate states of HIV-1 reverse transcriptase DNA synthesis
Authors: Vergara Sandra , Zhou Xiahong , Santiago Ulises , Conway James F , Sluis-Cremer Nicolas , Calero Guillermo 
Published: December 2023

AbstractReverse transcription of the retroviral single-stranded RNA into double-stranded DNA is an integral step during HIV-1 replication, and reverse transcriptase (RT) is a primary target for antiviral therapy. Despite a wealth of structural information on RT, we lack critical insight into the intermediate kinetic states of DNA synthesis. Using catalytically active substrates, and a novel blot/diffusion cryo-electron microscopy approach, we captured 11 structures that define the substrate binding, reactant, transition and product states of dATP addition by RT at 1.9 to 2.4 Å resolution in the active site. Initial dATP binding to RT-template/primer complex involves a single Mg2+(site B), and promotes partial closure of the active site pocket by a large conformational change in the β3-β4 loop in the Fingers domain, and formation of a negatively charged pocket where a second “drifting” Mg2+can bind (site A). During the transition state, the α-phosphate oxygen from a previously unobserved dATP conformer aligns with the site A Mg2+and the primer 3′-OH for nucleophilic attack. In the product state, we captured two substrate conformations in the active site: 1) dATP that had yet to be incorporated into the nascent DNA, and 2) an incorporated dAMP with the pyrophosphate leaving group coordinated by metal B and stabilized through H- bonds in the active site of RT. This study provides insights into a fundamental chemical reaction that impacts polymerase fidelity, nucleoside inhibitor drug design, and mechanisms of drug resistance.
A Bayesian active learning platform for scalable combination drug screens
Authors: Tosh Christopher , Tec Mauricio , White Jessica , Quinn Jeffrey F. , Ibanez Sanchez Glorymar , Calder Paul , Kung Andrew L. , Dela Cruz Filemon S. , Tansey Wesley 
Published: December 2023

AbstractLarge-scale combination drug screens are generally considered intractable due to the immense number of possible combinations. Existing approaches use ad hoc fixed experimental designs then train machine learning models to impute novel combinations. Here we propose BATCHIE, an orthogonal approach that conducts experiments dynamically in batches. BATCHIE uses information theory and probabilistic modeling to design each batch to be maximally informative based on the results of previous experiments. On retrospective experiments from previous large-scale screens, BATCHIE designs rapidly discover highly effective and synergistic combinations. To validate BATCHIE prospectively, we conducted a combination screen on a collection of pediatric cancer cell lines using a 206 drug library. After exploring only 4% of the 1.4M possible experiments, the BATCHIE model was highly accurate at predicting novel combinations and detecting synergies. Further, the model identified a panel of top combinations for Ewing sarcomas, all of which were experimentally confirmed to be effective, including the rational and translatable top hit of PARP plus topoisomerase I inhibition. These results demonstrate that adaptive experiments can enable large-scale unbiased combination drug screens with a relatively small number of experiments, thereby powering a new wave of combination drug discoveries. BATCHIE is open source and publicly available (https://github.com/tansey-lab/batchie).
Global organelle profiling reveals subcellular localization and remodeling at proteome scale
Authors: Hein Marco Y. , Peng Duo , Todorova Verina , McCarthy Frank , Kim Kibeom , Liu Chad , Savy Laura , Januel Camille , Baltazar-Nunez Rodrigo , Bax Sophie , Vaid Shivanshi , Vangipuram Madhuri , Ivanov Ivan E. , Byrum Janie R. , Pradeep Soorya , Gonzalez Carlos G. , Aniseia Yttria , Wang Eileen , Creery Joseph S. , McMorrow Aidan H. , Burgess James , Sunshine Sara , Yeung-Levy Serena , DeFelice Brian C. , Mehta Shalin B. , Itzhak Daniel N. , Elias Joshua E. , Leonetti Manuel D. 
Published: December 2023

ABSTRACTDefining the subcellular distribution of all human proteins and its remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immuno-capture coupled to mass spectrometry. We apply this proteomics workflow to a cell-wide collection of membranous and membrane-less compartments. A graph-based representation of our data reveals the subcellular localization of over 7,600 proteins, defines spatial protein networks, and uncovers interconnections between cellular compartments. We demonstrate that our approach can be deployed to comprehensively profile proteome remodeling during cellular perturbation. By characterizing the cellular landscape following hCoV-OC43 viral infection, we discover that many proteins are regulated by changes in their spatial distribution rather than by changes in their total abundance. Our results establish that proteome-wide analysis of subcellular remodeling provides essential insights for the elucidation of cellular responses. Our dataset can be explored atorganelles.czbiohub.org.
Evaluating the validity of the eye movement event detection model of Ganzin Sol glasses
Authors: Chien Sung-En , Lee Kueian , Chang Chia-Yang , Lu Shaw-Chun , Chien Shao-Yi 
Published: December 2023

AbstractEye tracking requires precise measurement of gaze data. Identifying fixations and saccades reliably is crucial for eye trackers, given these are fundamental eye movements. The present study evaluated the performance of Ganzin Sol glasses, a wearable eye tracker developed by Ganzin Technology, in detecting eye movement events. Participants performed the fixation and saccade invocation task (Komogortsev et al., 2010) and the gap paradigm (Saslow, 1967) using both Ganzin Sol and Tobii Pro 2 glasses separately at both short (50 cm) and long (300 cm) viewing distance. The fixation and saccade invocation task involved maintaining fixation on a regularly shifting visual target, enabling quantitative and qualitative analysis of participants’ oculomotor behaviors. In the gap paradigm, participants executed saccades toward a peripheral target when the fixation disappeared (gap condition) or remained visible (overlap condition). Typically, saccade latency in the gap condition is shorter (i.e., the gap effect). Results revealed aligned performances with Ganzin Sol and Tobii Pro 2 glasses in the fixation and saccade invocation task and the observation of the gap effect with both eye trackers. Therefore, the validity of Ganzin Sol glasses was at least comparable to Tobii Pro 2 glasses in the present study.
Towards understanding interactions in a complex world: Design and analysis of multi-species functional response experiments
Authors: Rosenbaum Benjamin , Li Jingyi , Hirt Myriam R. , Ryser Remo , Brose Ulrich 
Published: December 2023

AbstractThe functional response describes feeding rates of consumers as a function of resource density. While models for feeding on a single resource species are well studied and supported by a large body of empirical research, consumers feeding on multiple resource species are ubiquitous in nature. However, laboratory experiments designed for parameterizing multi-species functional responses (MSFR) are extremely rare, mainly due to logistical challenges and the non-trivial nature of their statistical analysis.Here, we describe how these models can be fitted to empirical data in a Bayesian framework. Specifically, we address the problem of prey depletion during experiments, which can be accounted for through dynamical modeling. In a comprehensive simulation study, we test the effects of experimental design, sample size and noise level on the identifiability of four distinct MSFR models. Additionally, we demonstrate the method’s versatility by applying it to a list of empirical datasets.We identify experimental designs for feeding trials that produce the most accurate parameter estimates in two- and three-prey scenarios. Although noise introduces systematic bias in parameter estimates, model selection performs surprisingly well for the four MSFRs, almost always identifying the correct model even for small datasets.This flexible framework allows the simultaneous analysis of feeding experiments from both single- and multi-prey scenarios, either with or without prey depletion. This will help to elucidate mechanisms such as prey selectivity, prey switching and their implications for food web stability and biodiversity. Our approach equips researchers with the appropriate statistical tools to improve the understanding of feeding interactions in complex ecosystems.
ARBUR, a machine learning-based analysis system for relating behaviors and ultrasonic vocalizations of rats
Authors: Chen Zhe , Jia Guanglu , Zhou Qijie , Zhang Yulai , Quan Zhenzhen , Chen Xuechao , Fukuda Toshio , Huang Qiang , Shi Qing 
Published: December 2023

AbstractDeciphering how different types of behavior and ultrasonic vocalizations (USVs) of rats interact can yield insights into the neural basis of social interaction. However, the behavior-vocalization interplay of rats remains elusive because of the challenges of relating the two communication media in complex social contexts. Here, we propose a machine learning-based analysis system (ARBUR) that can cluster without bias both non-step (continuous) and step USVs, hierarchically detect eight types of behavior of two freely behaving rats with high accuracy, and locate the vocal rat in 3-D space. By simultaneously recording the video and ultrasonic streams of two freely behaving rats, ARBUR reveals that rats communicate via distinct USVs when engaging in different types of social behavior. Moreover, we show that ARBUR can not only automatically reveal the well-understood behavior-associated vocalizations that were carefully concluded by other behavioral researchers, but also hold the promise to indicate novel findings that can be hardly found by manual analysis, especially regarding step USVs and the active/passive rat-associated USVs during easy-to-confuse social behaviors. This work highlights the potential of machine learning algorithms in automatic animal behavioral and acoustic analysis and could help mechanistically understand the interactive influence between the behaviors and USVs of rats.
Extended model to explain customer attitude toward NFT and moderating effect of technology optimism
Authors: Lee Won-jun 
Published: December 2023

PurposeThis study empirically examined consumer adoption attitudes and behaviors toward nonfungible tokens (NFTs). Findings indicate that consumer attitudes toward NFTs are influenced by perceived usefulness, reliability and profit expectancy and that strong attitudes are associated with purchase intentions. Additionally, the relationship between attitudes and purchase intentions was moderated by technology optimism.Design/methodology/approachThe authors utilized a partial least squares (PLS) model to examine the hypotheses in this empirical analysis. Obtaining a sample of actual NFT holders or experienced users is challenging. A total of 105 individuals participated in the study as valid responders by answering the screening question in the questionnaire. The authors opted for the PLS model as a research approach due to the limited size of the consumer population in the NFT market.FindingsThis study discovered that the adoption of NFTs was affected by technical aspects such as usefulness and reliability and the potential for future asset growth. Furthermore, the degree of attitude-to-intention conversion varied based on optimism, an inherent characteristic.Research limitations/implicationsThis study offers valuable insights for NFT owners, content providers and trading firms. For the NFT market to expand, it must meet consumers' expectations for the desired content features and asset investment attributes. Additionally, customer targeting strategies should attract and appeal to technology enthusiasts with an optimistic outlook on technology.Originality/valueThe authors conducted an initial empirical analysis of actual NFT consumers, an area of research studied sparingly despite its significance.
COVID-19 and the decline of active social media engagement
Authors: Poole Maxwell , Pancer Ethan , Philp Matthew , Noseworthy Theodore J. 
Published: December 2023

PurposeThe COVID-19 pandemic triggered an increase in online traffic, with many assuming that this technology would facilitate coping through active social connections. This study aims to interrogate the nature of this traffic-engagement relationship by distinguishing between passive (e.g. browsing) and active (e.g. reacting, commenting and sharing) engagement, and examining behavioral shifts across platforms.Design/methodology/approachThree field studies assessed changes in social media engagement during the COVID-19 pandemic. These studies included social media engagement with the most followed accounts (Twitter), discussion board commenting (Reddit) and news content sharing (Facebook).FindingsEven though people spent more time online during the pandemic, the current research finds people were actively engaging less. Users were reacting less to popular social media accounts, commenting less on discussion boards and even sharing less news content.Research limitations/implicationsWhile the current work provides a systematic observation of engagement during a global crisis, it does not claim causality based on its correlational nature. Future research should test potential mechanisms (e.g. anxiety, threat and privacy) to draw causal inference and identify possible interventions.Practical implicationsThe pandemic shed light on a complex systemic issue: the misunderstanding and oversimplification of how online platforms facilitate social cohesion. It encourages thoughtful consideration of online social dynamics, emphasizing that not all engagement is equal and that the benefits of connection may not always be realized as expected.Originality/valueThis research provides a postmortem on the traffic-engagement relationship, highlighting that increased online presence does not necessarily translate to active social connection, which might help explain the rise in mental health issues that emerged from the pandemic.
Sustainable performance among power companies in Uganda: role of stakeholder orientation, human capital, regulatory governance, and management control systems
Authors: Akankunda Brendah , Nkundabanyanga Stephen Korutaro , Adaramola Muyiwa Samuel , Kaawaase Twaha Kigongo 
Published: December 2023

Purpose
The purpose of this study is to investigate the connections between the regulatory governance, human capital, stakeholder orientation, management control systems (MCSs) and sustainable performance (SP) of power companies. The authors especially looked at how much regulatory governance, human capital, stakeholder orientation and MCSs affect the SP across power companies in Uganda.

Design/methodology/approach
This is a cross-sectional and correlational study. Data were collected from 105 power companies using a questionnaire and analysed using SPSS.

Findings
Stakeholder orientation, MCSs, human capital and regulatory governance significantly predict variances in the SP of power providers in Uganda. Stakeholder orientation is the most important predictor of SP of power companies.

Research limitations/implications
The absence of validation from important stakeholders and the major reliance on company-provided data in existing research on SP raises the possibility of self-desirability bias. To evaluate and verify the information supplied by firms with external stakeholders, further studies might consider using an explanatory mixed methods technique, in which quantitative data are initially gathered from the managers of power companies and analysed and then validated by interviews with important stakeholders.

Originality/value
Using stakeholder, legitimacy and resource-based theories has provided a better explanation for SP which is a multi-dimensional notion. Moreover, the study adds to the body of perception-based research that offers direct management incentives for SP. The perspectives of managers have been gathered through the use of self-administered questionnaires to gather impressions of managers of businesses, which has helped to tap into all aspects of SP. The study’s results offer, probably for the first time to the best of the authors’ knowledge, evidence of the contextual elements that affect SP in African nations like Uganda particularly in the power sector.
Institutional ownership stability and product quality failures
Authors: Le Thanh Dat , Nguyen Nguyen 
Published: December 2023

PurposeThis study examines the effect of stable institutional investors on firms' product quality failures. Furthermore, the authors investigate the channels through which institutional ownership stability enhances product quality management.Design/methodology/approachThis study uses probit, ordered probit and negative binomial regression frameworks to investigate the research questions. In addition, the authors utilize the three-stage least-squares to address the endogeneity issues.FindingsUsing a sample of product recall incidents from 2012 to 2021, the authors find that firms with more stable institutional ownership have a lower probability, frequency and severity of recall incidents and adopt a proactive product recall strategy. Institutional investors with significant and persistent holdings improve quality management by reducing overinvestment and the use of option-linked and relative performance executive compensations. Furthermore, the influence of stable institutional owners on product quality failures is more pronounced in firms with low managerial ability and specialist CEOs. Lastly, the empirical evidence demonstrates that stable holdings by active investors have a more substantial impact on reducing product recalls than passive and other stable institutional holdings.Originality/valueThis study is the first to examine the impact of institutional ownership stability on firms' product recalls. The authors contribute to the literature on the benefits of stable institutional ownership on firm outcomes and the determinants of product quality failures.
Empowering leadership and employee well-being: the role of psychological empowerment and time pressure
Authors: Tran Pham Toan Khanh 
Published: December 2023

PurposeLittle research has focused on empowering leadership (EL) in the context of public organizations. Thus, this study aims to explore the relationship between EL and public employees' well-being (EWB). In addition, utilizing a moderated mediation mechanism, this study investigates the mediating role of psychological empowerment (PE) and the moderating role of time pressure (TP) and collectivist orientation in the proposed model.Design/methodology/approachQuantitative data were collected from 643 public servants working in wards (grassroot-level government) in Vietnam. Partial least squares structural equation modeling (PLS-SEM) was employed to test the proposed relationships.FindingsThe results show that EL and PE have a significant positive effect on EWB. Moreover, PE has a complementary effect on this nexus. The results also lent credence to the moderating roles of TP and collectivist orientation.Practical implicationsThe empirical results of this inquiry provide valuable implications for public managers. The findings suggest that public managers can promote EWB by implementing EL and enhancing PE. Moreover, when designing and implementing tasks, managers should ensure sufficient time for their followers.Originality/valueThis study advances the understanding of public sector EWB via the predictive role of empowering leaders and the mediation mechanism of PE. Moreover, this study is among the pioneering studies exploring the moderating role of TP and collectivist orientation on these relationships.