bluuebunny/crossref_metadata_2025_split huggingface dataset:
Living xylem cells encode a large number of conserved gene families responsible for vascular sap peptides
Authors: Lu Min R. , Tung Chia-Chun , Huang Chia-En , Chen Chang-Hung , Liou Pin-Chien , Lin Chan-Yi Ivy , Yu Jhong-He , Chen Ying-Lan , Jimmy Lin Ying-Chung , Tsai Isheng Jason 
Published: November 2024

AbstractPlant long-distance signaling peptides travel through the vascular system to coordinate development and respond to environmental cues, yet their precursor genes and expression origins remain elusive. We characterized 4,804 sap peptide precursor genes inPopulus trichocarpausing an integrated approach that combined liquid chromatography tandem mass spectrometry (LC-MS/MS) peptidomics, transcriptomics, and comparative genomics. This study expands the known precursor families from approximately 50 to thousands, the majority of which are conserved across angiosperms. Transcriptome analysis across xylem developmental stages revealed that living xylem cells, typically viewed as precursors to non-living structures, predominantly express these specifically at transitions between primary and secondary growth stages, indicating an active role in plant-wide signaling coordination. The precursor genes show conservation at the transcriptome level and are under strong purifying selection. Our findings provide a comprehensive overview of the gene families encoding sap peptides, redefining xylem as an active participant in plant communication and adaptation.
Seasonal patterns in b-vitamins and cobalamin co-limitation in the Northwest Atlantic
Authors: Bannon Catherine , White Patrick L. , Rowland Elden , More Kiran J. , Gleason Anna , Roberts Megan , Devred Emmanuel , Beazley Lindsay , LaRoche Julie , Bertrand Erin M. 
Published: November 2024

AbstractB-vitamins are important co-enzymes that have long been hypothesized to play key roles in marine ecosystems. However, environmental measurements remain scarce, which limits our understanding of their potential impact. Here, we present mass spectrometry-based measurements of b-vitamins (B1, B2, B3, B5, B6,B12) and related vitamers along a transect in the Northwest Atlantic Ocean, in both particulate phase and dissolved in seawater, seasonally over 5 years, and couple this with targeted investigations of the impact of B12(cobalamin) on phytoplankton growth. We show that these metabolites are present at femto to pico-molar concentrations and demonstrate that season explains most variance in particulate phase b-vitamins but not dissolved, offering further evidence that metabolite inventories in these two phases are often decoupled. We find correlations between particulate organic carbon with particulate B1and B3, and between chlorophyllaand particulate B2and DMB in fall but not spring, indicating unique seasonal drivers of vitamin inventories. Of all measured vitamins, only cobalamin was enriched in the particulate over dissolved phase, predominantly in spring. We documented nitrogen and cobalamin co-limitation of phytoplankton growth during spring bloom decline, when dissolved cobalamin is seemingly drawn down, but not during fall, when dissolved cobalamin concentrations remain elevated. These seasonal differences may be underpinned by the increased importance of cobalamin remodeling and recycling during the fall. This study provides insights into the absolute concentrations, stoichiometry, and variability of b-vitamins in the ocean and offers evidence that cobalamin exerts seasonally-varying controls on Northwest Atlantic marine ecosystems.
Homocysteine thiolactone from translation proofreading is an endogenous ligand for cell-cell signaling by the receptor SdiA
Authors: Leiva Lorenzo Eugenio , Zuniga Roberto , Phillips Gregory J. , Ibba Michael 
Published: November 2024

AbstractSeveral widespread mechanisms enable cellular communication and coordinate the behavior of bacterial populations. The modules responsible for cellular communication are often found in matching pairs: an enzyme synthesizing a signal molecule and a specific receptor capable of decoding it. A notable exception isEscherichia coliSdiA, a homolog of known N-acyl homoserine lactone (AHL) receptors for which no corresponding AHL synthase exists. SdiA is an orphan receptor that enables cross-talk by sensing AHLs from other bacterial species. In this work, we investigated if homocysteine thiolactone (HTL), an AHL-like molecule arising from a proofreading reaction of methionyl tRNA synthetase (MetRS) to correct misactivation of homocysteine, participates inE. colicommunication through SdiA. A comprehensive analysis of MetRS variants producing different levels of HTL showed more extended lag periods due to lower HTL levels, which were restored by HTL supplementation. SdiA mutants abolished the regulation of the transition from the lag phase to the exponential phase induced by HTL. Growth phenotypes were HTL-specific and were not induced by supplementation of other non-endogenous AHLs previously characterized as SdiA ligands. The gene expression ofgadYandrmfregulated by SdiA was modulated by HTL supplementation. Through differential scanning fluorimetry, we show the SdiA-HTL interactionin vitro. Together, our observations describe HTL as an SdiA ligand capable of modulating cell-cell communication in bacteria.
In Silico Discovery of Multi-Target Natural Ligands and Efficient siRNA Design for Overcoming Drug Resistance in Breast Cancer via Local Therapy
Authors: Hashemi Seyed Mohammad Javad , Barzegar Ali , Akhtari Javad , Mellati Amir 
Published: November 2024

AbstractIn this study, we designed an efficient siRNA for PKMYT1 gene knockdown, and evaluated the binding affinities of different natural ligands to crucial proteins involved in breast cancer. Designed siRNA showed strong binding affinity and minimal off-target effects. Molecular docking studies identified new ligands as antagonists with high binding affinities for aromatase, estrogen receptor alpha, HER2, and PARP10, as well as agonists for MT2 and STING. The natural ligand SCHEMBL7562664 was introduced as a golden ligand due to its high affinity among multiple targets and lack of cytotoxic and mutagenic effects. Natural small molecules identified in this research, due to their multi-target characteristics, provided a solution to overcome the problem of drug resistance in cancer cells. Furthermore, the proposed three dimensional scaffold design for local breast cancer therapy offers a promising approach to increase the delivery and efficacy of these natural small molecules, reduce systemic side effects, and improve treatment outcomes. In this study, new ligands with significant binding affinities and favorable pharmacokinetic properties were identified, which paves the way for further research in targeted therapy of breast cancer.
Biophysical Basis of Paracellular Barrier Modulation by a Pan-Claudin-Binding Molecule
Authors: Ogbu Chinemerem P. , Mandriota Alexandria M. , Liu Xiangdong , de las Alas Mason , Kapoor Srajan , Choudhury Jagrity , Kossiakoff Anthony A. , Duffey Michael E. , Vecchio Alex J. 
Published: November 2024

AbstractClaudins are a 27-member protein family that form and fortify specialized cell contacts in endothelium and epithelium called tight junctions. Tight junctions restrict paracellular transport across tissues by forming molecular barriers between cells. Claudin-binding molecules thus hold promise for modulating tight junction permeability to deliver drugs or as therapeutics to treat tight junction-linked disease. The development of claudin-binding molecules, however, is hindered by their intractability and small targetable surfaces. Here, we determine that a synthetic antibody fragment (sFab) we developed binds directly to 10 claudin subtypes with nanomolar affinity by targeting claudin’s paracellular-exposed surface. Application of this sFab to cells that model intestinal epithelium show that it opens the paracellular barrier comparable to a known, but application limited, tight junction modulator. This novel pan-claudin-binding molecule can probe claudin or tight junction structure and holds potential as a broad modulator of tight junction permeability for basic or translational applications.
Cell position-based evaluation of mechanical features of cells in multicellular systems
Authors: Koyama Hiroshi , Ito Atsushi M. , Okumura Hisashi , Otani Tetsuhisa , Nakamura Kazuyuki , Fujimori Toshihiko 
Published: November 2024

AbstractMeasurement of mechanical forces of cell–cell interactions is important for studying the emergence of diverse three-dimensional morphologies of multicellular organisms. We previously reported an image-based statistical method for inferring effective pairwise forces of cell–cell interactions (i.e., attractive/repulsive forces), where a cell particle model was fitted to cell tracking data acquired by live imaging. However, because the particle model is a coarse-grained model, it remains unclear how the pairwise forces relates to sub-cellular mechanical components including cell–cell adhesive forces. Here we applied our inference method to cell tracking data generated by vertex models that assumed sub-cellular components. Through this approach, we investigated the relationship between the effective pairwise forces and various sub-cellular components: cell–cell adhesion forces, cell surface tensions, cell–extracellular matrix (ECM) adhesion, traction forces between cells and ECM, cell growth, etc. We found that the cell–cell adhesion forces were attractive, and both the cell surface tensions and cell–ECM adhesive forces were repulsive, etc. These results indicate that sub-cellular mechanical components can contribute to the effective attractive/repulsive forces of cell–cell interactions. This comprehensive analysis provides theoretical bases for linking the pairwise forces to the sub-cellular mechanical components: this showcase is useful for speculating the sub-cellular mechanical components from the information of cell positions, and for interpreting simulation results based on particle models.
Machine learning of honey bee olfactory behavior identifies repellent odorants in free flying bees in the field
Authors: Kowalewski Joel , Baer-Imhoof Barbara , Guda Tom , Luy Matthew , DePalma Payton , Baer Boris , Ray Anandasankar 
Published: November 2024

ABSTRACTPreventing beneficial insects like honey bees (Apis mellifera) from contacting pesticides on crops using odorants could counter current pollinator declines. However, the discovery of behaviorally aversive odorants is impeded by the complexity of the honey bee olfactory system where >180 odorant receptors detect volatiles and generate valence. To solve this systems-level challenge we generated a machine-learning model to predict aversive valence from chemical structure using published olfactory behavior data in honey bees. We refine the predictive model by generating species level behavioral data for honeybees andDrosophilaon an initial set of novel predicted repellents. The improved second computational model was then used to screen a chemical space of >50 million compounds and identify >130 repellent candidates. Behavioral validation using honey bees in the laboratory show a high predictive success. Additional testing of the top seven candidates using freely foraging honey bees in a field assay confirmed strong repellency, thus predicting a high probability to repel foraging bees from pesticide-treated crops. Machine learning, with iterative testing and modeling, therefore provides a powerful approach for rational discovery of aversive volatiles for control of insects for which limited data is available.SIGNIFICANCE STATEMENTWith honey bee populations declining partly due to pesticide exposure, we aimed to find smells that could keep bees away from pesticide treated crops. We overcome challenges studying the complex bee olfactory system by developing an AI model trained on existing bee behavior data to predict chemicals bees would find aversive. The predictive model screened millions of compounds, identifying more than 130 potential repellents. Behavior testing in the lab and in field tests confirmed the effectiveness of the bee repellents. This method could lead to bee-safe pesticide formulations, potentially protecting pollinator populations while maintaining crop protection.
Disproportionate regulation of wildlife trade
Authors: Challender Daniel W.S. , Mallon David , Sas-Rolfes Michael ‘t , Dickman Amy , Hare Darragh , Hart Adam G. , Mandisodza-Chikerema Roseline L. , Roe Dilys , Mbaiwa Joseph E. , Hoffmann Michael 
Published: November 2024

AbstractAn increasing number of countries in the Global North have enacted, or are considering, import bans on hunting trophies to protect wildlife. We interrogate arguments used to characterize trophy hunting using data from the Convention on International Trade in Endangered Species (CITES), the International Union for Conservation of Nature (IUCN) Red List of Threatened Species, and empirical research. We show that trophy hunting is not a major threat to any CITES-listed species traded as a trophy during 2000-2022. Yet, 60% of global trade in trophies involving these species may be impacted by bans, with significant implications for conservation. We therefore question whether such legislative actions are proportionate. Wildlife trade solutions may appear simple but evidence-based policy is needed to conserve biodiversity and avoid harming people.
Building bridges and the chance to do better tomorrow: global resource sharing moving forward
Authors: Cohen Lapis , Pang Xuan , McIntyre Joanne M. , Stanwicks Kabel Nathan 
Published: November 2024

Purpose
The purpose of this paper is to disseminate the American Library Association (ALA) Reference and User Services Association (RUSA) Sharing and Transforming Access to Resources Section (STARS) international interlibrary loan (ILL) Committee 2023 international ILL survey results and findings. The survey evaluates current international resource sharing operations, identifies trends and challenges and recommends promoting services within the global library community.

Design/methodology/approach
The survey used the Qualtrics platform and included multiple-choice and open-ended questions. The survey questionnaire was built upon the 2019 and 2015 instruments to facilitate longitudinal data analysis and comparison. The committee added new questions related to the COVID-19 pandemic and controlled digital lending (CDL). The survey was distributed to libraries worldwide via multiple channels, in all seven official International Federation of Library Associations and Institutions (IFLA) languages. Qualitative comparative analysis methodology was applied to analyze the survey results.

Findings
The survey results reveal the challenges and opportunities to engage in international ILL activities. The importance of sharing electronic resource content continues to grow as library collections shift from print to electronic resources.

Originality/value
The 2023 international ILL survey is the first offered in all seven official IFLA languages and included questions on the topics of COVID-19 and CDL. It contributes to the literature by providing global trends and perspectives on current international resource sharing practices, challenges and opportunities facing the global resource sharing community and recommendations on building bridges to do better in the future.
Emotion and cognition in customer experience: a mixed-method study on loyalty formation in the hospitality sector
Authors: Bujisic Milos , Li Yizhi “Ian” , Bilgihan Anil 
Published: November 2024

PurposeThis study investigates the dual roles of emotion and cognition in shaping customer experiences within the hospitality sector, examining their distinct impacts on the formation of customer loyalty.Design/methodology/approachEmploying a sequential exploratory mixed-method design, this research integrates qualitative interviews with eighteen hospitality managers and a quantitative survey involving 595 customers to develop and validate a new instrument measuring affective and cognitive experiential states for general hospitality consumers.FindingsThe study's results reveal that emotional experiences strongly correlate with affective loyalty, while cognitive experiences significantly influence cognitive loyalty. The study contributes to the existing literature by introducing a robust instrument that effectively captures the experiential dimensions, offering insights into customer loyalty formation.Research limitations/implicationsThe reliance on retrospective self-reporting in the quantitative phase may introduce recall bias, potentially limiting the precision of the findings. Future research should seek to mitigate this by employing real-time data capture methods.Practical implicationsThe newly developed measurement tool presents a practical solution for industry professionals aiming to enhance customer experience management by focusing on both affective and cognitive aspects, thus facilitating targeted strategies to cultivate customer loyalty. The implications for service design suggest that both emotional and cognitive elements must be considered to optimize customer experiences and drive loyalty.Originality/valueThis work advances the theoretical understanding of customer experience by distinguishing between its affective and cognitive dimensions and their respective contributions to loyalty. It offers a validated empirical tool, setting a foundation for future investigations.
Diagnosis of heart disease using an advanced triple hybrid algorithm combining machine learning techniques
Authors: Mostofi Shokoofa , Kordrostami Sohrab , Refahi Sheikhani Amir Hossein , Faridi Masouleh Marzieh , Shokri Soheil 
Published: November 2024

Purpose
This study aims to improve the detection and quantification of cardiac issues, which are a leading cause of mortality globally. By leveraging past data and using knowledge mining strategies, this study seeks to develop a technique that could assess and predict the onset of cardiac sickness in real time. The use of a triple algorithm, combining particle swarm optimization (PSO), artificial bee colony (ABC) and support vector machine (SVM), is proposed to enhance the accuracy of predictions. The purpose is to contribute to the existing body of knowledge on cardiac disease prognosis and improve overall performance in health care.

Design/methodology/approach
This research uses a knowledge-mining strategy to enhance the detection and quantification of cardiac issues. Decision trees are used to form predictions of cardiovascular disorders, and these predictions are evaluated using training data and test results. The study has also introduced a novel triple algorithm that combines three different combination processes: PSO, ABC and SVM to process and merge the data. A neural network is then used to classify the data based on these three approaches. Real data on various aspects of cardiac disease are incorporated into the simulation.

Findings
The results of this study suggest that the proposed triple algorithm, using the combination of PSO, ABC and SVM, significantly improves the accuracy of predictions for cardiac disease. By processing and merging data using the triple algorithm, the neural network was able to effectively classify the data. The incorporation of real data on various aspects of cardiac disease in the simulation further enhanced the findings. This research contributes to the existing knowledge on cardiac disease prognosis and highlights the potential of leveraging past data for strategic forecasting in the health-care sector.

Originality/value
The originality of this research lies in the development of the triple algorithm, which combines multiple data mining strategies to improve prognosis accuracy for cardiac diseases. This approach differs from existing methods by using a combination of PSO, ABC, SVM, information gain, genetic algorithms and bacterial foraging optimization with the Gray Wolf Optimizer. The proposed technique offers a novel and valuable contribution to the field, enhancing the competitive position and overall performance of businesses in the health-care sector.
Aerial litter mimicry: A novel form of floral deception mediated by a monoterpene synthase
Authors: Liu Ming‐Fai , Chen Junhao , Goodrich Katherine R. , Chiu Sung Kay , Pang Chun‐Chiu , Scharaschkin Tanya , Saunders Richard M. K. 
Published: November 2024

Abstract

Floral mimics deceive their pollinators by developing visual and olfactory resemblance to various models. We report a flower that exhibits phenotypes like aerial litter and deceives an aerial litter specialist beetle to achieve pollination.

We assessed the floral phenology and the effective pollinators of an Australian understorey treelet, Meiogyne heteropetala (Annonaceae). The similarities of morphology, colour and odour between the flowers and co‐occurring aerial litter were investigated. The terpene synthase involved in floral scent emission was identified by expression patterns and product profile. The behavioural responses of the pollinator to various odours were assessed using bioassays.

The erotylid beetle Loberus sharpi is the most likely effective pollinator because it was the only pollen‐laden visitor during the pistillate phase. Loberus sharpi was exclusively found in aerial litter and M. heteropetala flowers. The flowers offer an honest shelter reward. The beetle also oviposits there, but most larvae eventually perished as the petals dropped onto the forest floor. The morphology and spectral reflectance of the flowers overlap with aerial litter. The floral scent was dominated by monoterpenes, especially 1,8‐cineole. The cineole synthase MhCINS was the only highly expressed floral terpene synthase and possessed a highly similar product profile to the floral scent composition. The volatile composition of M. heteropetala flowers is distinct from other congeners and highly similar to aerial litter, indicating advergence to aerial litter. Visual and odour resemblance, coupled with low larval survivorship, provides evidence that the beetles were deceived into pollinating the flowers. Behavioural experiments showed that the pollinator was attracted to both aerial litter and M. heteropetala flowers. The beetles were also attracted to 1,8‐cineole and synthetic mixes of floral odour and MhCINS products. The beetles were unable to distinguish floral scent from MhCINS products nor from 1,8‐cineole, suggesting MhCINS alone sufficed to attract the pollinator olfactorily. The beetles, however, preferred aerial litter over flowers. The beetles likely categorised the flower as a general, but not the most preferred, brood substrate.

Synthesis. This study reports the first case of floral mimicry of aerial litter and characterises the biochemical process responsible for olfactory mimicry.