bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular basis for the assembly of the dynein transport machinery on microtubules
Authors: Rao Qinhui , Chai Pengxin , Zhang Kai 
Published: January 2025

AbstractCytoplasmic dynein-1, a microtubule-based motor protein, requires dynactin and an adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The role of microtubules in DDA assembly has been elusive. Here, we reveal detailed structural insights into microtubule-mediated DDA assembly using cryo-electron microscopy. We find that an adaptor-independent dynein- dynactin complex (DD) predominantly forms on microtubules in an intrinsic 2:1 stoichiometry, induced by spontaneous parallelization of dynein upon microtubule binding. Adaptors can squeeze in and exchange within the assembled microtubule-bound DD complex, which is enabled by relative rotations between dynein and dynactin, and further facilitated by dynein light intermediate chains that assist in an adaptor ‘search’ mechanism. Our findings elucidate the dynamic adaptability of the dynein transport machinery, and reveal a new mode for assembly of the motile complex.
Imaging-based screen identifies novel natural compounds that perturb cell and chloroplast division inChlamydomonas reinhardtii
Authors: Clark-Cotton Manuella R. , Chen Sheng-An , Gomez Aracely , Mulabagal Aditya , Perry Adriana , Malhotra Varenyam , Onishi Masayuki 
Published: January 2025

ABSTRACTSuccessful cell division requires faithful division and segregation of organelles into daughter cells. The unicellular algaChlamydomonas reinhardtiihas a single, large chloroplast whose division is spatiotemporally coordinated with furrowing. Cytoskeletal structures form in the same plane at the midzone of the dividing chloroplast (FtsZ) and the cell (microtubules), but how these structures are coordinated is not understood. Previous work showed that loss of F-actin blocks chloroplast division but not furrow ingression, suggesting that pharmacological perturbations can disorganize these events. In this study, we developed an imaging platform to screen natural compounds that perturb cell division while monitoring FtsZ and microtubules and identified 70 unique compounds. One compound, curcumin, has been proposed to bind to both FtsZ and tubulin proteins in bacteria and eukaryotes, respectively. InC. reinhardtii,where both targets coexist and are involved in cell division, curcumin at a specific dose range caused a severe disruption of the FtsZ ring in chloroplast while leaving the furrow-associated microtubule structures largely intact. Time-lapse imaging showed that loss of FtsZ and chloroplast division failure delayed the completion of furrowing but not the initiation, suggesting that the chloroplast-division checkpoint proposed in other algae requires FtsZ or is absent altogether inC. reinhardtii.SIGNIFICANCE STATEMENTSuccessful cell division requires the coordination of both organelle inheritance and cytokinesis. The unicellular algaChlamydomonas reinhardtii, which spatiotemporally coordinates the division of its chloroplast with cytokinesis, is an excellent model to study the regulation.We screened libraries of natural compounds for perturbations of cell and/or chloroplast division, identifying 70 unique chemicals. By time-lapse microscopy using one of the hits, curcumin, we demonstrate that although chloroplast division failures delay the completion of cytokinesis, it does not impair initiation.These findings suggest that the chloroplast-division checkpoint proposed in other algae requires FtsZ or is absent altogether inC. reinhardtii.
Fusobacterium nucleatumis enriched in invasive biofilms in colorectal cancer
Authors: Queen Jessica , Cing Zam , Minsky Hana , Nandi Asmita , Southward Taylor , Ferri Jacqueline , McMann Madison , Iyadorai Thevambiga , Vadivelu Jamuna , Roslani April , Loke Mun Fai , Wanyiri Jane , White James R. , Drewes Julia L. , Sears Cynthia L. 
Published: January 2025

AbstractFusobacterium nucleatumis an oral bacterium known to colonize colorectal tumors, where it is thought to play an important role in cancer progression. Recent advances in sequencing and phenotyping ofF. nucleatumhave revealed important differences at the subspecies level, but whether these differences impact the overall tumor ecology, and tumorigenesis itself, remain poorly understood. In this study, we sought to characterizeFusobacteriain the tumor microbiome of a cohort of individuals with CRC through a combination of molecular, spatial, and microbiologic analyses. We assessed for relative abundance ofF. nucleatumin tumors compared to paired normal tissue, and correlated abundance with clinical and pathological features. We demonstrate striking enrichment ofF. nucleatumand the recently discovered subspeciesanimalisclade 2 (Fna C2) specifically in colon tumors that have biofilms, highlighting the importance of complex community partnerships in the pathogenesis of this important organism.
Introducing and Evaluating the Patient Report Template for AI-Powered Nursing Handoffs
Authors: Vald Gabriel , Sermet Yusuf , Chi Nai-Ching , Demir Ibrahim 
Published: January 2025

AbstractThis study evaluates the effectiveness of the Patient Report Template (PRT) in addressing inefficiencies in nursing workflows related to electronic health records (EHRs) and clinical decision support systems. The PRT aims to streamline patient handoffs, reduce charting time, enhance direct care hours, and improve patient safety. A survey was sent to 2,118 nurses at the University of Iowa Health Care System in order to gather feedback, with 106 participants electing to assess the perceived usefulness of the PRT components and their attitudes toward integrating artificial intelligence (AI) into clinical documentation. Participants rated sections of the PRT, including Patient Profile, Review of Systems, and Safety, on a five-point Likert scale, with most components receiving high ratings for usefulness. Comfort and trust in AI were notably low, though respondents acknowledged the potential utility of AI-generated reports. The findings highlight the PRT’s potential to reduce cognitive load, improve information consistency during handoffs, and address EHR-related challenges. Future work will involve implementing the PRT in real-world clinical settings to validate its utility & accuracy and to explore its adaptability across specialized nursing units.What is knownElectronic health records and clinical decision support systems carry burdens associated with data retrieval and entry, as well as introduce more friction to clinical workflow.Electronic health record data is vast; free text clinical notes are abundant and underused.While crucial for care continuity, handoffs often lack standardization and thus are prone to information loss and safety risks.What this paper addsCreation and feedback on a clinical decision support template which aims to reduce pain points associated with charting.Feedback from 106 University of Iowa Health Care nurses about what they would and would not find useful in a patient handoff report.Pathway to further usability and accuracy testing for reports which make use of items from the patient report template.
Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment
Authors: Boulay Alexandre , Leprince Audrey , Enault François , Rousseau Elsa , Galiez Clovis 
Published: January 2025

AbstractBacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of protein sequences. Consequently, the majority of functions carried by phage proteins remain elusive. Current tools to comprehensively identify phage protein functions from their sequence either lack sensitivity (those relying on homology for instance) or specificity (assigning a single coarse grain function to a protein). Here, we introduce Empathi, a protein-embedding-based classifier that assigns functions in a hierarchical manner – from general functional categories such as “structural” and “DNA-associated” proteins to more specific ones including “nucleases”, “tail appendages” and “endolysins” to name only a few. These categories were specifically tailored for phage protein functions and organized such that molecular-level functions are respected in each category, making it well suited for training machine learning classifiers based on protein embeddings. We show on a dataset of cultured phage genomes that Empathi significantly outperforms homology-based methods, tripling the number of annotated homologous groups. On the EnVhog database, the most recent and extensive database of metagenomically-sourced phage proteins, Empathi doubled the annotated fraction of protein families from 16% to 33%. On complete genomes taken from new viromes, almost twice as many proteins are annotated using our method, predictions are consistent when compared to existing tools and Empathi predictions are highly colocalized. In addition, by leveraging Empathi’s ability to assign multiple labels to the same protein, it is possible to identify multifunctional proteins such as virion-associated lysins. Having a more global view of the repertoire of functions a phage possesses will assuredly help to understand them and their interactions with bacteria better.
Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer’s disease neuropathology
Authors: Rodriguez-Rodriguez Patricia , Wang Wei , Tsagkogianni Christina , Feng Irena , Morello-Megias Ana , Jain Kaahini , Alanko Vilma , Kahvecioglu Han-Ali , Mohammadi Elyas , Li Xiaofei , Flajolet Marc , Sandebring-Matton Anna , Maioli Silvia , Vidal Noemi , Milosevic Ana , Roussarie Jean-Pierre 
Published: January 2025

AbstractNeurons located in layer II of the entorhinal cortex (ECII) are the primary site of pathological tau accumulation and neurodegeneration at preclinical stages of Alzheimer’s disease (AD). Exploring the alterations that underlie the early degeneration of these cells is essential to develop therapies that curb the disease before symptom onset. Here we performed cell-type specific profiling of human EC at the onset of AD neuropathology. We identify an early response to amyloid pathology by microglia and oligodendrocytes. Importantly, we provide the first insight into neuronal alterations that coincide with incipient tau pathology: the signaling pathway for Reelin, recently shown to be a major AD resilience gene is dysregulated in ECII neurons, while the secreted synaptic organizer molecules NPTX2 and CBLN4, emerging AD biomarkers, are downregulated in surrounding neurons. By uncovering the complex multicellular landscape of EC at these early AD stages, this study paves the way for detailed characterization of the mechanisms governing NFT formation and opens long-needed novel therapeutic avenues.
Dynamic connectedness, hedge and safe-haven effects: cryptocurrencies, precious metals and African stock markets
Authors: Korsah David , Mensah Lord , Osei Kofi Achampong , Amewu Godfred 
Published: January 2025

PurposeThis study seeks to: (1) examine the extent of interconnectedness prevailing between the cryptocurrency market, the stock market and the precious metals market. (2) Conduct thorough assessment of hedge and safe-haven qualities of broad range of precious metals and cryptocurrencies against returns on the African stock market.Design/methodology/approachThis study applied two novel approaches that is Cross-quantilogram, an advanced statistical technique used to examine the relationship between quantiles of response variable and the quantiles of predictor variables, and TVP-VAR, a technique that captures the dynamic connectedness of variables under consideration.FindingsIt was found that the three markets are highly interconnected, particularly among assets under the respective financial markets. It was further revealed that the Johannesburg Stock Exchange (JSE) was the most resilient stock market, whereas Bitcoin, BNB, Silver (XAG) and Platinum (XPT) also exhibited notable resistance to shocks. Finally, the study found that cryptocurrencies and precious metals portrayed varying hedge and safe haven qualities under the various stock markets.Practical implicationsThe high interdependency between the African stock market, cryptocurrencies and precious metals suggests that none of the markets is immune to shocks form the other market. The finding that cryptocurrencies and precious metals exhibit some degree of safe-haven and hedge potentials, albeit limited in certain stock markets, provides investors with alternative investment options during market downturns. Since most African stock markets, except the JSE, are net receivers of shocks, investors in these markets should exercise caution during periods of global financial uncertainty.Originality/valueTo the best of our knowledge, this study is the first to explore the dynamic interconnectedness between seven carefully selected African stock markets, three distinct cryptocurrencies and four precious metals, while also assessing the hedge and safe-haven potential of the cryptocurrencies and precious metals against stock market returns. Additionally, the study stands out in recent literature by employing two novel approaches: the TVP-VAR model, which captures the dynamic connectedness among variables, and the Cross-Quantilogram, an advanced statistical method that analyzes the relationship between the quantiles of the response and predictor variables, all within a single study.
Service robot–employee task allocation strategies: well-being within the intrusion challenge
Authors: Phillips Chelsea , Odekerken-Schröder Gaby , Russell-Bennett Rebekah , Steins Mark , Mahr Dominik , Letheren Kate 
Published: January 2025

PurposePrevious research has not considered the impact on human frontline employees (FLEs) of altered employee–customer relationships in the presence of a service robot (i.e. an intrusion challenge), nor how FLEs may respond. The purpose of this study is to explore the task allocation strategies by human frontline employees’ (FLE) work well-being responses within the intrusion challenge.Design/methodology/approachThis study employs a mixed-method approach, whereby an in-depth qualitative study (Study 1, n = 15) is followed by a quantitative field study (Study 2, n = 81).FindingsResults indicate that FLEs experience the intrusion challenge, impacting social, purpose, physical and community well-being. Study 1 reveals that while service robots trigger this challenge, FLEs use them for task allocation to maintain their initial work well-being state. Study 2 shows that using robots instead of colleagues positively affects FLE work well-being.Practical implicationsService robots, as a task allocation strategy by FLEs, can be used to empower FLEs by assisting them to preserve their work well-being within the intrusion challenge.Originality/valueThis study is one of the first to involve FLEs from a live service robot site, where data is based on personal lived experiences rather than anticipated experiences. This is the first study to investigate how FLEs respond to the intrusion challenge.
Dynamic selection of cooperative partners of agricultural science and technology industry-university-research system based on field theory
Authors: Zhang Yanwei , Lu Xinhai , Li Jinqiu , Lin Chaoran 
Published: January 2025

PurposeAgricultural science and technology (AST) often need the form of industry-university-research cooperation in successfully completing breakthrough agricultural technology innovations. Therefore, AST industry-university-research cooperation is not only the need of the AST development strategy in China but also the only way for the development of agricultural colleges and universities, agricultural scientific research institutions and agricultural enterprises. Among them, in the process of cooperative breakthrough agricultural technology innovation, the correct selection of partners is the basis for ensuring its effective operation.Design/methodology/approachAiming at the time-series characteristics and information ambiguity of decision information in the dynamic selection process of AST industry-university-research partners, this research introduces the dynamic intuitionistic fuzzy multi-criteria decision-making method of time degree and orthogonal projection. On this basis, field theory is used to construct the cooperative innovation capability field model of the partners, and the threshold for the partners to enter or exit the system is designed to dynamically select and eliminate the partners.FindingsResults show that this method fully considers the situation of cooperative innovation resources within the AST industry-university-research system and the resource complementarity of candidate partners.Originality/valueCombined with examples from agricultural scientific research institutions, the applicability and superiority of the model are verified.
Osimertinib for EGFR‐Mutant NSCLC Patients With Acquired T790M and EGFR Amplification After First‐Generation EGFR‐TKI Resistance
Authors: Zhang Yidan , Xu Yingqi , Xu Jianlin , Zhong Hua , Xia Jinjing , Zhong Runbo 
Published: January 2025

ABSTRACTThird‐generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR‐TKI) is the standard therapy for patients harboring T790M after first‐generation EGFR‐TKI resistance. However, the impact of acquired EGFR amplification on the efficacy of third‐generation EGFR‐TKI against T790M remains uncertain. We aimed to investigate whether the presence of acquired EGFR amplification after first‐generation EGFR‐TKI resistance influences the efficacy of third‐generation EGFR‐TKI in patients with advanced non‐small‐cell lung cancer (NSCLC). We reviewed data from 275 advanced NSCLC patients harboring T790M after first‐generation EGFR‐TKI resistance. Patients were categorized into two groups based on the presence or absence of acquired EGFR amplification identified through next‐generation sequencing (NGS) after first‐line EGFR‐TKI treatment. We evaluated the efficacy of osimertinib used as a second‐line treatment. Among these patients, 59 exhibited acquired EGFR amplification, while 216 did not. The median progression‐free survival (PFS) was 12.20 months in the EGFR amplification group and 12.03 months in the non‐amplification group (p = 0.011), with median overall survival (OS) of 33.90 months and 23.30 months, respectively (p = 0.164). Multivariate analysis of PFS revealed that acquired EGFR amplification and EGFR 19del were independent prognostic factors for patients with T790M undergoing osimertinib. Additionally, subgroup analysis indicated a prolonged PFS in patients with EGFR 19del compared to those with EGFR 21L858R (p = 0.034) in the EGFR amplification group. Following first‐generation EGFR‐TKI resistance, advanced EGFR‐mutant NSCLC patients harboring both acquired T790M and EGFR amplification are likely to experience enhanced PFS with osimertinib. This phenomenon is particularly noteworthy among individuals with EGFR 19del.
The Continuity‐Contiguity Problem in Fragmentation‐Biodiversity Research
Authors: Dennis M. , Huck J. J. 
Published: January 2025

ABSTRACTA primary question for researchers in the field of conservation science concerns the fragmentation of biodiversity‐supporting habitat. Key debates revolve around the relevance of habitat composition and configuration for conservation outcomes. Central to this debate is the measurement and delineation of the habitat patch, which informs fragmentation‐related metrics and their evaluation. Despite the need to quantify and model habitat fragmentation, the habitat patch concept itself has been subject to criticism concerning its ability to adequately reflect the heterogeneity of resource distributions in complex landscapes. In this paper, we present the continuity‐contiguity problem, which is one of the fundamental challenges related to the delineation of habitat in space, and discuss its implications for fragmentation‐biodiversity research. We outline the potential contribution of recent developments in spatial‐ecological methods and the leveraging of uncertainty in the modelling process to address four common issues related to the habitat patch concept: the gap‐crossing problem, the need for multi‐variate habitat delineation, the delineation of interior‐edge transitions and the need to parameterise habitat as both a discrete and continuous spatial entity. We conclude with several recommendations for studies on fragmentation‐biodiversity outcomes where the continuity‐contiguity problem may influence the research process.
“Electrohydrodynamic Drying: A Comprehensive Review of Design Considerations and Quality Effects on Dried Fruits and Vegetables”
Authors: Prakasha R. , Vinay G. M. , Pandey H. , Bhoi Paresh M. 
Published: January 2025

ABSTRACTElectrohydrodynamic (EHD) drying, an emerging non‐thermal technology, gains favor for its simple construction, energy efficiency, and superior dried product quality. Operating at ambient temperature, it preserves a product's original characteristics. This study delves into EHD drying's mechanism, electrode selection, and design considerations, emphasizing its impact on vitamins, color, and bioactive compounds in fruits and vegetables. A comparative analysis with traditional and innovative drying methods is included, exploring combined and EHD‐assisted techniques for improved organoleptic and nutritional qualities. While, currently it is limited to lab‐scale, scaling up EHD drying holds promise for ensuring nutritional security, with considerations on various limiting factors and future potential.
“When you leave out the door”: The streets, Medicaid, and boundary spaces of healthcare in urban poverty
Authors: Ziv Tali 
Published: January 2025

AbstractAttending closely to the lived experiences of people moving in and out of Medicaid‐funded institutions, I argue that “the streets” are critical to understanding healthcare in US urban poverty. Exploring the relationship between “the streets” and Medicaid‐funded institutions, this essay asks: How does the relationship between “the streets”—and in the words of my research interlocutors—“life on the other side” shape life in Medicaid‐funded institutions in the Northeast US city? How do the social and symbolic conditions of this relationship—conditions structured by anti‐Blackness—formulate the human in urban poverty? By joining Medicaid‐funded institutions together as a broader health‐governing network, I demonstrate how these institutions become boundary spaces that reveal the socially and symbolically interdependent worlds of “the streets” and life off them. Ultimately, this essay argues that “the streets” contain the social and symbolic conditions that dehumanize the poor through the logics of anti‐Blackness, thus defining the terms of humanization that Medicaid‐funded institutions afford.