bluuebunny/crossref_metadata_2025 huggingface dataset:
Systematic identification and characterization of virus lncRNAs suggests extensive structural mimicry of host lncRNAs
Authors: Fu Ping , Cai Zena , You Ruina , Deng Lei , Li Zhaoyong , Miao Zhichao , Peng Yousong
Published: November 2024

Virus long non-coding RNAs (vlncRNAs) play crucial roles in viral infections, yet their identification and characterization remain limited. This study identified 5,053 novel vlncRNAs across 25 viral species using third-generation sequencing, with two from Influenza A virus and Vesicular stomatitis virus validated by RT-qPCR. Most vlncRNAs originated from dsDNA viruses. Only 1% having annotated RNA families, suggesting many novel RNA structures. Although only seven vlncRNAs shared sequence similarities with human lncRNAs (hlncRNAs), 772 vlncRNAs from 15 human viruses structurally mimicked hlncRNAs. These vlncRNA and hlncRNAs bound to similar miRNAs, potentially acting as miRNA sponges to promote essential life process. Splicing analysis showed vlncRNAs had a prevalence of alternative first exon. Finally, we developed vlncRNAbase (http://computationalbiology.cn/vlncRNAbase/#/) to store and organize the newly identified and known vlncRNAs. Overall, the study provides a valuable resource for further investigation into vlncRNAs and deepens our understanding of the diversity, structure and function of the molecule.
The safety and efficacy of Ultrasound Histotripsy and human pluripotent stem cell-derived hepatic spheroid implantation as a potential therapy for treatment of congenital metabolic liver disease: assessment in an immunocompetent rodent model
Authors: Rashidi Hassan , Khalil Amjad , Froghi Saied , Hall Andrew , Gelat Pierre , Davidson Brian , Quaglia Alberto , Saffari Nader
Published: November 2024

Background

Liver disease secondary to an inborn or genetic error of metabolism is a rare group of conditions often associated with chronic ill health and reduced survival. Curative treatment is mainly limited to liver transplantation with major long-term risks. Cell therapy is a promising alternative, but current approaches are ineffective.

Aim

To develop histotripsy, a non-invasive high intensity ultrasound procedure for liver tissue mechanical ablation, combined with hepatocyte stem cell implantation as a novel method of reversing liver failure from genetic disease. This study assessed the safety and feasibility of this approach in healthy rodents.

Methods

Under general anaesthesia, adult rats (n=12) underwent laparotomy and ultrasound histotripsy to the exposed liver. Around 1 million cells were injected into a single histotripsy cavity in each animal under direct vision (n=10) with two receiving only histotripsy without cell injection. On completion of cell implant haemostasis was secured, laparotomy incision closed, and the animals recovered. Groups of animals were terminated immediately and after 4 hrs, 8 hrs, 24hrs, 4 days and 7 days. Liver and vital organs were assessed for procedure related injuries and evidence of viable implanted cells by histology and immunohistochemistry.

Results

All animals successfully recovered, and no complication was observed throughout the study. Created cavities were successfully identified in histological analysis of rat. The presence of human cells was verified using anti-human nuclei antibody confirming successful implantation of liver organoids into decellularized cavities.

Conclusions

In this feasibility study, we demonstrated suitability of histotripsy to create decellularized cavities in liver parenchyma. In addition, feasibility of direct transplantation of undissociated liver organoids into the created cavities was demonstrated as a potential approach to treat inborn liver disease by creating nodules of healthy cells capable of performing loss metabolic function. Therapeutic efficacy of this approach will be evaluated in an upcoming study.
Uncovering hidden gene-trait patterns through biclustering analysis of the UK Biobank
Authors: Pividori Milton , Sadeeq Suraju , Krishnan Arjun , Stranger Barbara E. , Gignoux Christopher R.
Published: November 2024

The growing availability of genome-wide association studies (GWAS) and large-scale biobanks provides an unprecedented opportunity to explore the genetic basis of complex traits and diseases. However, with this vast amount of data comes the challenge of interpreting numerous associations across thousands of traits, especially given the high polygenicity and pleiotropy underlying complex phenotypes. Traditional clustering methods, which identify global patterns in data, lack the resolution to capture overlapping associations relevant to subsets of traits or genes. Consequently, there is a critical need for innovative analytic approaches capable of revealing local, biologically meaningful patterns that could advance our understanding of trait comorbidities and gene-trait interactions. Here, we applied BiBit, a biclustering algorithm, to transcriptome-wide association study (TWAS) results from PhenomeXcan, a large resource of gene-trait associations derived from the UK Biobank. BiBit allows simultaneous grouping of traits and genes, identifying biclusters that represent local, overlapping associations. Our analyses uncovered biologically interpretable patterns, including asthma-related biclusters enriched for immune-related gene sets, connections between eye traits and blood pressure, and associations between dietary traits, high cholesterol, and specific loci on chromosome 19. These biclusters highlight gene-trait relationships and patterns of trait co-occurrence that may otherwise be obscured by traditional methods. Our findings demonstrate that biclustering can provide a nuanced view of the genetic architecture of complex traits, offering insights into pleiotropy and disease mechanisms. By enabling the exploration of complex, overlapping patterns within biobank-scale datasets, this approach provides a valuable framework for advancing research on genetic associations, comorbidities, and polygenic traits.
Enhanced lentiviral gene delivery to mammalian cells via paired cell surface and viral envelope engineering
Authors: Tannir Ryan , Chan Letitia , Grzywa Tomasz M. , Arevalo Orlando , Neeser Alexandra , Kahn Sara , Cozzone Austin , Olenick Lauren , Mason Nicola J , Ma Leyuan
Published: November 2024

Lentiviral vectors that facilitate gene delivery to desired cell types have been widely used in routine laboratory research and therapeutic cell engineering. However, the lack of proper entry receptors on many cell types often results in poor gene delivery. Here, we present a simple paired virus-cell engineering approach that promotes lentiviral gene delivery into mammalian cells. Lentiviruses are dual-pseudotyped with VSV-G and a chimeric envelope protein specifically recognizing a small molecule fluorescein (αFITC-Env), and target cells are transiently labelled with FITC to create surrogate receptors for lentivirus attachment. The synthetic interaction between FITC-labeled cells and FITC-binding LVs enables efficient LV docking, viral entry and stable transgene expression in a range of mammalian cell lines and primary T cells. We showed that this approach enabled efficient delivery of a CD19-targeted chimeric antigen receptor (CAR) into naïve human T cells that are naturally refractory to conventional VSV-G LVs, which upon activation rapidly eradicated CD19+leukemic cells. This paired cell surface and virus envelope engineering approach may serve as a universal method for engineering synthetic virus-cell interactions to improve lentiviral gene delivery to mammalian cells.
Aggregation of Transthyretin by Fluid Agitation
Authors: Ritsch Irina , Dyson H. Jane , Wright Peter E.
Published: November 2024

The transthyretin (TTR) tetramer, assembled as a dimer of dimers, transports thyroxine and retinol binding protein in blood plasma and cerebrospinal fluid. Aggregation of wild type or pathogenic variant TTR leads to transthyretin amyloidosis (ATTR), which is associated with neurodegenerative and cardiac disease. The trigger for TTR aggregation under physiological conditions is unknown. The tetramer is extremely stable at neutral pH, but aggregation via tetramer dissociation and monomer misfolding can be inducedin vitroby lowering the pH. To elucidate factors that may cause TTR aggregation at neutral pH, we examined the effect of shear forces such as arise from fluid flow in the vascular system. Fluid shear forces were generated by rapidly stirring TTR solutions in conical microcentrifuge tubes. Under agitation, TTR formed β-rich aggregates and fibrils at a rate that was dependent upon protein concentration. The lag time before the onset of agitation-induced aggregation increases as the total TTR concentration is increased, consistent with a mechanism in which the tetramer first dissociates to form monomer that either partially unfolds to enter the aggregation pathway or reassociates to form tetramer. NMR spectra recorded at various time points during the lag phase revealed growth of an aggregation-prone intermediate trapped as a dynamically perturbed tetramer. Enhanced conformational fluctuations in the weak dimer-dimer interface suggests loosening of critical inter-subunit contacts which likely destabilizes the agitated tetramer and predisposes it towards dissociation. These studies provide new insights into the mechanism of aggregation of wild type human TTR under near physiological conditions.
WITHDRAWN: Neutralizing Activity and Viral Escape of Pemivibart by SARS-CoV-2 JN.1 sublineages
Authors: Yao Tianjiao , Ma Zhenghai , Lan Ke , Guo Yicheng , Liu Lihong
Published: November 2024

Withdrawal Statement

The authors have withdrawn this manuscript because of a conflict of interest. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Fifteen-year Alcohol Consumption Trajectories and Their Association with Cardiovascular Events and Mortality: the Framingham Heart Study
Authors: Leng Yuanming , Ding Huitong , Li Yi , Liu Xue , Wang Mengyao , Lyu Chenglin , Levy Daniel , Ma Jiantao , Liu Chunyu
Published: November 2024

Background

Long-term alcohol consumption patterns play a critical role in human health.

Objectives

We aimed to identify alcohol consumption trajectories and analyze their associations with coronary heart disease (CHD) and all-cause mortality in the Framingham Heart Study (FHS).

Methods

We used a growth mixture model to identify sex-specific alcohol consumption trajectories over 15 years and Cox regression to examine associations of these trajectories with incident events that occurred during an additional 10-year follow-up, adjusting for covariates.

Results

We identified four distinct trajectory groups among 6,570 participants (mean age 52; 55% women): Group 1 (n=2,713, reference) consisted of low-level drinkers; Group 2 (n=1,818) mainly included abstainers; Groups 3 (n=805) and 4 (n=1,234) comprised drinkers with varying patterns, with Group 4 consuming the most. Over 10 years of follow-up, women in Groups 2 to 4 had hazard ratios (HR) for CHD of 1.57 (95% CI = 1.11-2.22), 1.57 (95% CI = 1.08-2.29), and 1.27 (95% CI = 1.05-1.55) compared to Group 1. Women in

Groups 2 (HR = 1.26, 95% CI = 1.05-1.50) and 3 (HR = 1.27, 95% CI = 1.05-1.55) also had higher all-cause mortality risks. Men in Group 2 had higher mortality (HR = 1.18, 95% CI = 1.02-1.37, P = 0.030) and CHD (HR = 1.56, 95% CI = 1.07-1.52, P = 0.001) risks compared to Group 1, while men in Group 4 had the highest mortality risk (HR = 1.27, 95% CI = 1.02-1.37).

Conclusion

This study identified four distinct alcohol consumption trajectories and demonstrated that maintaining low to moderate levels of alcohol drinking over time is likely associated with a lower risk of CHD and mortality in both women and men.
AlphaFold-Metainference: Prediction of Structural Ensembles of Disordered Proteins
Authors: Brotzakis Z. Faidon , Zhang Shengyu , Murtada Mhd Hussein , Vendruscolo Michele
Published: November 2024

Deep learning methods of predicting protein structures have reached an accuracy comparable to that of high-resolution experimental methods. It is thus possible to generate accurate models of the native states of hundreds of millions of proteins. An open question, however, concerns whether these advances can be translated to disordered proteins, which should be represented as structural ensembles because of their heterogeneous and dynamical nature. To address this problem, we introduce the AlphaFold-Metainference method to use AlphaFold-derived distances as structural restraints in molecular dynamics simulations to construct structural ensembles of ordered and disordered proteins. The results obtained using AlphaFold-Metainference illustrate the possibility of making predictions of the conformational properties of disordered proteins using deep learning methods trained on the large structural databases available for folded proteins.
Improved precision, sensitivity, and adaptability of Ordered Two-Template Relay cDNA library preparation for RNA sequencing
Authors: Ferguson Lucas , Upton Heather E. , Pimentel Sydney C. , Jeans Chris , Ingolia Nicholas T. , Collins Kathleen
Published: November 2024

Sequencing RNAs that are biologically processed or degraded to less than ∼100 nucleotides typically involves multi-step, low-yield protocols with bias and information loss inherent to ligation and/or polynucleotide tailing. We recently introduced Ordered Two-Template Relay (OTTR), a method that captures obligatorily end-to-end sequences of input molecules and, in the same reverse transcription step, also appends 5′ and 3′ sequencing adapters of choice. OTTR has been thoroughly benchmarked for optimal production of microRNA, tRNA and tRNA fragments, and ribosome-protected mRNA footprint libraries. Here we sought to characterize, quantify, and ameliorate any remaining bias or imprecision in the end-to-end capture of RNA sequences. We introduce new metrics for the evaluation of sequence capture and use them to optimize reaction buffers, reverse transcriptase sequence, adapter oligonucleotides, and overall workflow. Modifications of the reverse transcriptase and adapter oligonucleotides increased the 3′ and 5′ end-precision of sequence capture and minimized overall library bias. Improvements in recombinant expression and purification of the truncatedBombyx moriR2 reverse transcriptase used in OTTR reduced non-productive sequencing reads by minimizing bacterial nucleic acids that compete with low-input RNA molecules for cDNA synthesis, such that with miRNA input of 3 picograms (less than 1 fmol), fewer than 10% of sequencing reads are bacterial nucleic acid contaminants. We also introduce a rapid, automation-compatible OTTR protocol that enables gel-free, length-agnostic enrichment of cDNA duplexes from unwanted adapter-only side products. Overall, this work informs considerations for unbiased end-to-end capture and annotation of RNAs independent of their sequence, structure, or post-transcriptional modifications.
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

Plant 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.
Oceanic photosynthesis is directly affected by cyanophage NblA proteins
Authors: Nadel Omer , Hanna Rawad , Rozenberg Andrey , Shitrit Dror , Tahan Ran , Pekarsky Irena , Béjà Oded , Kleifeld Oded , Lindell Debbie
Published: November 2024

Marine picocyanobacteria are abundant photosynthetic organisms of global importance. They coexist in the ocean with cyanophages, viruses that infect cyanobacteria. Cyanophages carry many auxiliary metabolic genes acquired from their hosts that are thought to redirect host metabolism for the phage’s benefit1–5. One such gene isnblAwhich is present in multiple cyanophage families2,6–9. Under nutrient deprivation the cyanobacterial NblA is responsible for inducing proteolytic degradation of the phycobilisome10–12, the large cyanobacterial photosynthetic light harvesting complex. This increases the pool of amino acids available for essential tasks12, serving as a survival mechanism13. Ectopic expression of different cyanophagenblAgenes results in host pigment protein degradation9,7,6. However, the benefit of the cyanophage-encoded NblA for the cyanophage and the broader impact on the host are unknown. Here, using a recently developed genetic manipulation system for cyanophages14, we reveal that cyanophage NblA significantly accelerates the cyanophage infection cycle, directs degradation of the host phycobilisome and other photosynthetic proteins and reduces host photosynthetic light harvesting efficiency. Furthermore, metagenomic analysis revealed that cyanophages carryingnblAare widespread in the oceans and compose 35% and 65% of oceanic T7-like cyanophages in the surface and deep photic zones, respectively. Our results show a large benefit of thenblAgene to the cyanophage while exerting a negative effect on the host photosynthetic apparatus and host photosynthesis. These findings suggest thatnblA-encoding cyanophages have a global effect on the amount of light harvested by oceanic picocyanobacteria.
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

B-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

Several 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

In 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

Claudins 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

Measurement 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

Preventing 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 STATEMENT

With 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

An 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

Purpose

This 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/approach

Employing 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.

Findings

The 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/implications

The 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 implications

The 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/value

This 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

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.
Effects of wheat gluten–soy protein ratios and moisture levels on high‐moisture extruded meat analogues for burger patties
Authors: Dubey Aishwary , Kumar Arun , Singh Narpinder
Published: November 2024

In response to the growing demand for plant‐based meat alternatives, this study explores the impact of incorporating wheat gluten (WG) into soy protein isolate (SPI) on both the proximate and functional properties of protein blends. The research also examines the effects of high moisture extrusion processing, varying feed moisture levels (60%, 65%, and 70%), and WG‐SPI blends on extruder response, as well as the textural, rheological, and solubility characteristics of the resulting extruded meat analogues. Moreover, the prime objective was to gain insights into the impact of using HMMA made at different ratios and feed moisture levels on plant‐based burgers. As the WG incorporation level increased in SPI, the RVA viscosity, water absorption, and oil absorption capacities, and foaming stability exhibited a decrease while foaming capacity increased. As feed moisture and WG incorporation levels in SPI increased, the system parameters, rheological, and textural parameters of high moisture extruded meat analogs decreased. WG25‐SPI75 showed the highest degree of texturization or sulfide bonds, and its extruded meat analogues at 60% feed moisture level burger patties resemble a similar textural to a chicken burger patty. This study is pivotal in understanding how wheat gluten in SPIs and feeding moisture level influence the textural and rheology properties of HMMA.
Characteristics of whey protein concentrate/egg white protein composite film modified by transglutaminase and its application on cherry tomatoes
Authors: Jiang Shujuan , Zhang Jiaxin , Zhang Mengyuan , Qian Fang , Mu Guangqing
Published: November 2024

In order to obtain food packaging film with better performance, whey protein concentrate (WPC) and egg white protein (EWP) were used as film‐forming substrates, and its film properties were modified by transglutaminase (TG). Then the effect of TG on the mechanical, physical, barrier, and microstructural properties of the WPC/EWP composite biodegradable film was investigated, and its preliminary application potential was explored. Compared to WPC and EWP films, WPC/EWP composite film had higher transmittance, tensile strength (TS), and thermal stability. Fluorescence results showed that the film experienced fluorescence quenching after TG treatment. Fourier transform infrared and x‐ray diffraction results showed that WPC and EWP had good compatibility in the biodegradable film, the hydrogen bond interaction of film was increased due to TG, resulting in an increase in TS. Meanwhile, the water vapor permeability and contact angle of WPC/EWP film treated with TG at 5 U/g protein increased by 28% and 76.1%, respectively. Besides, the WPC/EWP biodegradable film modified by TG (TG‐W/E) was applied as a coating film on cherry tomatoes, effectively reducing the weight loss rate during storage from 14.2% to 10.8%. Furthermore, indexes, such as solid content, spoilage rate, hardness, pH, and lycopene, showed that the film had a good preservation effect on cherry tomatoes. To conclude, the appropriate addition of TG has a positive effect on the film properties of the WPC/EWP biodegradable film, which is beneficial to the development and utilization of protein‐based film. WPC/EWP biodegradable film modified by TG has a great application prospect in extending the shelf life of fruit and vegetable.
Switching to reusable operating theatre equipment: lessons learnt from sterile light handle projects in two Australian hospitals
Authors: Chen Stanley , McAlister Scott , Colagiuri Philomena , Pickles Kristen , Barratt Alexandra L.
Published: November 2024

Background

Replacing single‐use operating theatre equipment with reusables might be one strategy for reducing the carbon footprint of operating theatres. However, in Australia, where the energy mix is predominantly fossil‐fuel‐based, the re‐sterilization of reusables may increase the carbon footprint. We analyzed the financial and environmental impacts of introducing reusable operating theatre light handles in two NSW hospitals.

Methods

The effects on cost, waste, and carbon footprint of replacing disposable light handle covers with reusable handles in each hospital were analyzed over 12 months using procurement, waste and sterilization data, and life cycle assessment.

Results

Energy requirement for sterilization of reusable handles, increasing alongside weight of the handle, resulted in higher carbon footprint than using disposable covers. At one hospital, using a heavy handle increased carbon emissions sixfold, while the cost of handle sterilization exceeded the cost of disposable covers, resulting in 11% higher cost per use. At the other hospital, using a lighter handle increased carbon emissions by 40% per use, while sterilization cost was less than the cost of disposable covers, resulting in 14.8% lower cost per use. Scenario modelling indicated that sterilizing handles as part of a hollowware set rather than as individual items would significantly reduce cost and carbon footprint. At both hospitals, associated clinical waste was essentially eliminated.

Conclusion

Judicious replacement of disposable covers with lightweight yet durable reusable handles can reduce costs, but increases carbon footprint in the current Australian energy context. Adopting predominantly renewable energy and more efficient sterilization practice would mitigate this.
Paediatric bone marrow mesenchymal stem cells support acute myeloid leukaemia cell survival and enhance chemoresistance via contact‐independent mechanism
Authors: Laing Alison , Elmarghany Ahmed , Alghaith Arwa A. , Gouma Aya , Stevens Thomas , Winton Alexander , Cassels Jennifer , Clarke Cassie J. , Schwab Claire , Harrison Christine J. , Gibson Brenda , Keeshan Karen
Published: November 2024

Children diagnosed with acute myeloid leukaemia (paediatric AML [pAML]) have limited treatment options and relapse rates due to chemoresistance and refractory disease are over 30%. Current treatment is cytotoxic and in itself has long‐lasting harsh side effects. New, less toxic treatments are needed. The bone marrow microenvironment provides chemoprotection to leukaemic cells through cell communication and interaction with mesenchymal stem cells (MSCs), but this is not well defined in pAML. Using primary patient material, we identify a cell contact‐independent mechanism of MSC‐mediated chemoprotection involving extrinsic soluble factors that is abrogated through inhibition of the JAK/STAT and ERK pathways.
Long‐term tracking of haematopoietic clonal dynamics and mutations in non‐human primate undergoing transplantation of lentivirally barcoded haematopoietic stem and progenitor cells
Authors: Hosuru Rohan V. , Yang Jack , Zhou Yifan , Gin Ashley , Hayal Taha B. , Hong So Gun , Dunbar Cynthia E. , Wu Chuanfeng
Published: November 2024

Haematopoietic stem and progenitor cell (HSPC) autologous gene therapies are promising treatment for a variety of blood disorders. Investigation of the long‐term HSPC clonal dynamics and other measures of safety and durability following lentiviral‐mediated gene therapies in predictive models are crucial for assessing risks and benefits in order to inform decisions regarding wider utilization. We established an autologous lentivirally barcoded HSPC transplantation model in rhesus macaque (RM), a model offering insights into haematopoiesis and gene therapies with direct relevance to human. Healthy young adult RMs underwent total body irradiation, followed by transplantation of autologous HSPCs transduced with a lentiviral vector containing a diverse genetic barcode library, uniquely labelling individual HSPCs and their progeny. With up to 131 months of follow‐up, we now report quantitative clonal dynamics, characterizing the number, diversity, stability and lineage bias of hundreds of thousands of HSPC clones tracked in five RMs. We documented long‐term stable and multi‐lineage output from a highly polyclonal pool of HSPCs. Clonal succession after stable haematopoietic reconstitution was minimal. There was no evidence for accelerated acquisition of acquired somatic mutations following autologous lentivirally transduced HSPC transplantation. Our results provide relevant insights into long‐term HSPC behaviours in vivo following transplantation and gene therapies.