bluuebunny/crossref_metadata_2025 huggingface dataset:
Plant BCL-Domain Homologues play a conserved role in SWI/SNF complex stability
Authors: Candela-Ferre Joan , Pérez-Alemany Jaime , Diego-Martin Borja , Pandey Vijaya , Wohlschlegel James A. , Lozano-Juste Jorge , Gallego-Bartolomé Javier
Published: September 2024

The SWItch/Sucrose Non-Fermenting (SWI/SNF) complexes are evolutionarily conserved, ATP-dependent chromatin remodelers crucial for multiple nuclear functions in eukaryotes. Recently, plant BCL-Domain Homolog (BDH) proteins were identified as shared subunits of all plant SWI/SNF complexes, significantly impacting chromatin accessibility and various developmental processes in Arabidopsis. In this study, we performed a comprehensive characterization ofbdhmutants, revealing a previously overlooked impact on hypocotyl cell elongation. Through detailed analysis of BDH domains, we identified a plant-specific N-terminal domain that facilitates the interaction between BDH and the rest of the complex. Additionally, we uncovered the critical role of the BDH β-hairpin domain, which is phylogenetically related to metazoan BCL7 SWI/SNF subunits. While phylogenetic analyses did not identify BDH/BCL7 orthologs in fungi, structure prediction modeling demonstrated strong similarities between the SWI/SNF catalytic modules of plants, animals, and fungi, and revealed the yeast Rtt102 protein as a structural homolog of BDH and BCL7. This finding is supported by the ability of Rtt102 to interact with the Arabidopsis catalytic module subunit ARP7 and partially rescue thebdhmutant phenotypes. Further experiments revealed that BDH promotes the stability of the ARP4-ARP7 heterodimer, leading to the partial destabilization of ARP4 in the SWI/SNF complexes. In summary, our study unveils the molecular function of BDH proteins in plant SWI/SNF complexes and suggests that β-hairpin-containing proteins are evolutionarily conserved subunits crucial for ARP heterodimer stability and SWI/SNF activity across eukaryotes.
Hypoperfusion Profiles in outcome after Endovascular Therapy for Isolated Internal Carotid Artery Occluded Patients
Authors: Shi Feina , Chen Yigang , Zheng Xu , Jiang Yun , Xu Ziqi , Wang En , Wu Changzhu , Xu Chuan , Gao Qingqing , Hu Xi , Zhang Jinhua
Published: September 2024

Background

Patients with acute symptomatic isolated internal carotid artery occlusions (iICAO), also known as ICA-I occlusion, frequently presented with minor neurological deficits. However, they remained at risk for subsequent neurological deterioration even after intravenous thrombolysis. The efficacy of endovascular treatment (EVT) in iICAO patients remains uncertain. Recently, some retrospective studies revealed EVT for acute iICAO was safe and might confer potential benefits. Our aim was to identify the hypoperfusion profiles associated with neurological deterioration and functional outcome following EVT in iICAO patients.

Methods

We performed a multi-center, real-world cohort study involving acute symptomatic iICAO patients who underwent EVT from August 2018 to February 2024 across 3 stroke centers. Hypoperfusion profiles were assessed using Tmaxvolumes (>4s, >6s, >8s, and >10s) and Tmaxmismatch ratios (>10s/>8s, >10s/>6s, >10s>4s, >8s/>6s, >8s/>4s, and >6s/>4s). Neurological deterioration was defined as an increase of ⩾4 points in the NIHSS score prior to EVT. Good outcome was defined as modified Rankin Score 0 - 1 at 90 days.

Results

A total of 63 patients were included in the final analysis. Multivariable models showed that a lower Tmaxratio of >6s/>4s was an independent predictor for increased risk of neurological deterioration (OR, 0.003; 95% CI: 0.000-0.133; P = 0.003) and was associated with a better outcome following EVT (OR, 0.066; 95% CI: 0.005-0.874; P = 0.039) after adjustment. The optimal threshold for the Tmax>6s/>4s ratio was identified as 0.5.

Conclusions

A perfusion defect severity ratio of Tmax>6s/>4s less than 0.5 might indicate the likelihood of neurological deterioration, yet it would be associated with achieving a good outcome following EVT for iICAO patients. The hypoperfusion profile characterized by a Tmax>6s/>4s might be useful to the neurointerventionists for facilitating appropriate patient triage and guiding prognosis for EVT in iICAO patients.
WITHDRAWN: Filovirus outbreak responses and occupational health effects of chlorine spraying in healthcare workers: a systematic review and meta-analysis of alternative disinfectants and application methods
Authors: Fontana Luca , Stabile Luca , Caracci Elisa , Chaillon Antoine , Ait-Ikhlef Kamal , Buonanno Giorgio
Published: September 2024

Withdrawal statement

The authors have withdrawn this manuscript because of data issues that affect the validity of the findings. 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.
APEX2 proximity labeling of RNA in bacteria
Authors: Yassine Hadi , Schrader Jared M.
Published: September 2024

Rapid spatially controlled methods are needed to investigate RNA localization in bacterial cells. APEX2 proximity labeling was shown to be adaptable to rapid RNA labeling in eukaryotic cells, and through the fusion of APEX2 to different proteins targeted to different subcellular locations, has been useful to identify RNA localization in these cells. Therefore, we adapted APEX2 proximity labeling of RNA to bacterial cells by generating an APEX2 fusion to the RNase E gene, which is necessary and sufficient for BR-body formation. APEX2 fusion is minimally perturbative and RNA can be rapidly labeled on the sub-minute timescale with Alkyne-Phenol, outpacing the rapid speed of mRNA decay in bacteria. Alkyne-Phenol provides flexibility in the overall downstream application with copper catalyzed click-chemistry for downstream applications, such as fluorescent dyeazides or biotin-azides for purification. Altogether, APEX2 proximity labeling of RNA provides a useful method for studying RNA localization in bacteria.

Motivation

Studies over the past several years have shown that distinct RNAs can be targeted to subcellular locations in bacterial cells. The ability to investigate localized RNAs in bacteria is currently limited to imaging-based approaches or to laborious procedures to isolate ribonucleoprotein complexes by grad-seq, HITS-CLIP, or Rloc-seq. However, a major challenge in studying mRNA localization in bacterial cells is that bacterial mRNAs typically last for only a few minutes in the cell, while experiments to investigate their localization or interaction partners can take much longer. Therefore, rapid methods of studying RNA localization are needed to bridge this technical challenge.

Highlights

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APEX2 proximity labeling can be applied to RNA in bacteria

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APEX2 RNA labeling reactions occur on the sub-minute timescale.

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APEX2 workflow requires less material and time than current methods.

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Alkyne-Phenol APEX2 substrate provides flexibility with click-chemistry.
Systematic genome-guided discovery of antagonistic interactions between archaea and bacteria
Authors: Strock Romain , Soo Valerie WC , Hocher Antoine , Warnecke Tobias
Published: September 2024

The social life of archaea is poorly understood. In particular, even though competition and conflict are common themes in microbial communities, there is scant evidence documenting antagonistic interactions between archaea and their abundant prokaryotic brethren: bacteria. Do archaea specifically target bacteria for destruction? If so, what molecular weaponry do they use? Here, we present an approach to infer antagonistic interactions between archaea and bacteria from genome sequence. We show that a large and diverse set of archaea encode peptidoglycan hydrolases, enzymes that recognize and cleave a structure – peptidoglycan – that is a ubiquitous component of bacterial cell walls but absent from archaea. We predict the bacterial targets of archaeal peptidoglycan hydrolases using a structural homology approach and demonstrate that the predicted target bacteria tend to inhabit a similar niche to the archaeal producer, indicative of ecologically relevant interactions. Using a heterologous expression system, we demonstrate that two peptidoglycan hydrolases from the halophilic archaeaonHalogranum salariumB-1 kill the halophilic bacteriumHalalkalibacterium halodurans,a predicted target, and do so in a manner consistent with peptidoglycan hydrolase activity. Our results suggest that, even though the tools and rules of engagement remain largely unknown, archaeal-bacterial conflicts are likely common, and we present a roadmap for the discovery of additional antagonistic interactions between these two domains of life. Our work has implications for understanding mixed microbial communities that include archaea and suggests that archaea might represent a large untapped reservoir of novel antibacterials.
DNA replication dynamics are associated with genome composition inPlasmodiumspecies
Authors: Totañes Francis Isidore Garcia , Chapman Sarah E. , Rai Subash Kumar , Jones Mathew J. K. , Boemo Michael A. , Merrick Catherine J.
Published: September 2024

Plasmodiumspecies have variable genome compositions: many have an A/T-content of at least 80% while others are similar in composition to human cells. Here, we made a direct comparison of DNA replication dynamics in twoPlasmodiumspecies whose genomes differ by ∼20% A/T-content. This yielded fundamental insights into how DNA composition may affect replication. The highly A/T-biased genome ofP. falciparumshowed unusual replication dynamics that were not observed in the more balancedP. knowlesi– which had dynamics more like those of human cell lines. We observed that replication forks moved 50% slower inP. falciparumthan inP. knowlesi.InP. falciparum, replication forks slowed down over the course of S-phase whereas inP. knowlesi, fork speed increased as in human cells. Furthermore, in bothP. knowlesiand human cells, replication forks were strikingly slowed by sequences of particularly high A/T-bias, but inP. falciparum, although replication forks were inherently slow, they were not particularly slow in such biased sequences. Thus, the replisome ofP. falciparummay have evolved alongside its extremely biased genome, making it unusually robust to sequence bias. Since several antimalarial drugs act to stall DNA replication, this study may have implications for the effectiveness of, and development of, antimalarial therapies.
Craters on the melanoma surface facilitate tumor-immune interactions and demonstrate pathologic response to checkpoint blockade in humans
Authors: Ludin Aya , Stirtz Georgia L. , Tal Asaf , Nirmal Ajit J. , Besson Naomi , Jones Stephanie M. , Pfaff Kathleen L. , Manos Michael , Liu Sophia , Barrera Irving , Gong Qiyu , Rodrigues Cecilia Pessoa , Sahu Aditi , Jerison Elizabeth , Alessi Joao V. , Ricciuti Biagio , Richardson Douglas S. , Weiss Jodi D. , Moreau Hadley M. , Stanhope Meredith E. , Afeyan Alexander B. , Sefton James , McCall Wyatt D. , Formato Emily , Yang Song , Zhou Yi , Hoytema van Konijnenburg David P. , Cole Hannah L. , Cordova Miguel , Deng Liang , Rajadhyaksha Milind , Quake Stephen R. , Awad Mark M. , Chen Fei , Sorger Peter K. , Hodi F. Stephen , Rodig Scott J. , Murphy George F. , Zon Leonard I.
Published: September 2024

Immunotherapy leads to cancer eradication despite the tumor’s immunosuppressive environment. Here, we used extended long-term in-vivo imaging and high-resolution spatial transcriptomics of endogenous melanoma in zebrafish, and multiplex imaging of human melanoma, to identify domains that facilitate immune response during immunotherapy. We identified crater-shaped pockets at the margins of zebrafish and human melanoma, rich with beta-2 microglobulin (B2M) and antigen recognition molecules. The craters harbor the highest density of CD8+T cells in the tumor. In zebrafish, CD8+T cells formed prolonged interactions with melanoma cells within craters, characteristic of antigen recognition. Following immunostimulatory treatment, the craters enlarged and became the major site of activated CD8+T cell accumulation and tumor killing that was B2M dependent. In humans, craters predicted immune response to ICB therapy, showing response better than high T cell infiltration. This marks craters as potential new diagnostic tool for immunotherapy success and targets to enhance ICB response.
Glycoinformatic profiling of label-free intact heparan sulfate oligosaccharides
Authors: Maciej-Hulme Marissa L. , Kim Jandi , Roberts Elijah T. , Zhang Yiqing , van der Velden Anouk , den Braanker Dirk , Yanginlar Cansu , de Graaf Mark , Rabelink Ton , van den Berg Bernard , van Omen Ellen , Maas Rutger , van de Logt Anne-Els , Amster I. Jonathan , van der Vlag Johan
Published: September 2024

Heparan sulfates (HS) are a group of heterogenous linear, sulfated polysaccharides that play a role in in health and many diseases including cancer, cardiovascular, and kidney diseases. The structural variety of HS has greatly challenged the development and utility of HS analytics, particularly for native structures, leaving a significant gap in HS technologies for clinical application. Mass spectrometry (MS)-based profiling with bioinformatics offers a top-down approach that can retain variety in large data sets. Using healthy human plasmas, we developed an MS glycoprofiling approach for native HS oligosaccharides, which retains the structural complexity of each individual HS chain and generates an HS ‘index’ (or Heparan-ome) for each patient. As a proof of concept, analysis of 56 plasma samples ranging from 6 groups of kidney disease patients revealed a new subset cluster (20%, 4/20) of membranous glomerulopathy (MG) patients with distinct HS profiles, highlighting the potential of HS glycoprofiling as a powerful new approach into clinical practice, which warrants future development into clinical diagnostics of kidney and other diseases.

Graphical abstract
Cell attachment and tail contraction ofS. aureusphage phi812
Authors: Bíňovský Ján , Šiborová Marta , Nováček Jiří , Bárdy Pavol , Baška Roman , Škubník Karel , Botka Tibor , Benešík Martin , Pantůček Roman , Tripsianes Konstantinos , Plevka Pavel
Published: September 2024

Phages with contractile tails employ elaborate strategies to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Most tailed phages that have been structurally characterized to date infect Gram-negative bacteria, but those targeting Gram-positive bacteria, many of which are important human pathogens, are less well understood. Here, we show that the baseplate of phage phi812, which infects Gram-positive Staphylococcus aureus, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins type 1 and 2 and tripod complexes. Upon binding to the S. aureus cell wall, the symmetry of the baseplate transforms from threefold to sixfold. The conformational changes propagate from the outer edge to the core of the baseplate. The receptor-binding proteins re-orient to bind to the host cell. Subsequently, central spike proteins degrade teichoic acids. The conformational changes to the tripod complexes trigger the release of the central spike and weld proteins from the baseplate, which enables the hub proteins to cleave cell wall peptidoglycan and facilitate penetration of the tail tube tip through the cell membrane. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring formed by the tail sheath initiator proteins expands in diameter and thus triggers the contraction of the tail sheath. The tail sheath of phi812, which can bend up to 90° in its native conformation, shortens from 200 to 96 nm, which pushes the tail tube 10-30 nm into the cytoplasm, depending on the local thickness of the S. aureus cell wall. Our results provide the foundation for engineering phi812 to target specific S. aureus strains.
Kinetic regulation of kinesin’s two motor domains coordinates its stepping along microtubules
Authors: Niitani Yamato , Matsuzaki Kohei , Jonsson Erik , Vale Ronald D. , Tomishige Michio
Published: September 2024

The two identical motor domains (heads) of dimeric kinesin-1 move in a hand-over-hand process along a microtubule, coordinating their ATPase cycles such that each ATP hydrolysis is tightly coupled to a step and enabling the motor to take many steps without dissociating. The neck linker, a structural element that connects the two heads, has been shown to be essential for the head-head coordination; however, which kinetic step(s) in the chemomechanical cycle is “gated” by the neck linker remains unresolved. Here, we employed pre-steady state kinetics and single molecule assays to investigate how the neck linker conformation affects kinesin’s motility cycle. We show that the backward-pointing configuration of the neck linker in the front kinesin head confers higher affinity for microtubules, but does not change ATP binding and dissociation rates. In contrast, the forward-pointing configuration of the neck linker in the rear kinesin head decreases the ATP dissociation rate but has little effect on microtubule dissociation. In combination, these conformation-specific effects of the neck linker favor ATP hydrolysis and dissociation of the rear head prior to microtubule detachment of the front head, thereby providing a kinetic explanation for the coordinated walking mechanism of dimeric kinesin.
Clustering large-scale biomedical data to model dynamic accumulation processes in disease progression and anti-microbial resistance evolution
Authors: Dauda Kazeem A. , Aga Olav N. L. , Johnston Iain G.
Published: September 2024

Accumulation modelling uses machine learning to discover the dynamics by which systems acquire discrete features over time. Many systems of biomedical interest show such dynamics: from bacteria acquiring resistances to sets of drugs, to patients acquiring symptoms during the course of progressive disease. Existing approaches for accumulation modelling are typically limited either in the number of features they consider or their ability to characterise interactions between these features – a limitation for the large-scale genetic and/or phenotypic datasets often found in modern biomedical applications. Here, we demonstrate how clustering can make such large-scale datasets tractable for powerful accumulation modelling approaches. Clustering resolves issues of sparsity and high dimensionality in datasets but complicates the intepretation of the inferred dynamics, especially if observations are not independent. Focussing on hypercubic hidden Markov models (HyperHMM), we introduce several approaches for interpreting, estimating, and bounding the results of the dynamics in these cases and show how biomedical insight can be gained in such cases. We demonstrate this ‘Cluster-based HyperHMM’ (CHyperHMM) pipeline for synthetic data, clinical data on disease progression in severe malaria, and genomic data for anti-microbial resistance evolution inKlebsiella pneumoniae, reflecting two global health threats.
Vibrational resonance in bichromatically excited diatomic molecules in a shifted molecular potential
Authors: Abamba O. G. , Kolebaje O. T. , Vincent U. E. , McClintock P. V. E.
Published: September 2024

For bichromatically excited diatomic molecules modeled in a shifted Tietz-Wei molecular potential, we demonstrate the occurrence of vibrational resonance (VR) when a saddle-node (SN) bifurcation takes place and its nonoccurrence in the absence of an SN bifurcation. We have examined the VR phenomenon and its connection with SN bifurcation for eight diatomic molecules, namely, H2, N2, Cl2, I2, O2, HF, CO, and NO, consisting of homogeneous, heterogenous, and halogen molecules. We demonstrate that each of them vibrates at a distinct resonant frequency but with a spread in frequency. The high-frequency amplitude at which VR occurs corresponds to the SN-bifurcation point. We validate our analytic results by numerical simulations and show that the homonuclear halogens respond only weakly to bichromatic fields, which may perhaps be linked to their absence of SN bifurcation.

Published by the American Physical Society
2024
Dynamic entity formed by protein and its hydration water
Authors: Ye Yongfeng , Chen Xiaoxia , Huang Juan , Zheng Lirong , Tang Qingxue , Long Liuliu , Yamada Takeshi , Tyagi Madhusudan , Sakai Victoria García , O’Neill Hugh , Zhang Qiu , de Souza Nicolas R. , Xiao Xiang , Zhao Weishu , Hong Liang , Liu Zhuo
Published: September 2024

The interaction between protein and water plays a pivotal role in shaping the structure, dynamics, and function of biomacromolecules. A comprehensive understanding of this intricate interplay necessitates a systematic evaluation of interaction strength and its consequential impact on the dynamics of proteins and water across diverse protein systems. Despite numerous works on understanding the dynamics of water and proteins and the coupling between them, there are still unanswered questions. Here, we combine neutron scattering and isotope labeling to probe the dynamics of proteins and their hydration water in a variety of protein systems. We consider proteins of different structures and varying thermostability as well as proteins within living cells with distinct growth temperatures. Simultaneous characterization of protein and hydration water dynamics across diverse systems was achieved. Moreover, we performed water sorption isothermal measurements on three representative proteins to correlate the observed dynamics with the strength of the interaction energies governing each system. The experimental results underscore that proteins manifesting stronger attractive interactions with water display diffusionlike dynamics with higher flexibility upon hydration, concomitant with a reduced mobility in hydration water. Significantly, our findings suggest that, in fact, it is the interaction between protein and its hydration water that facilitates the transfer of mobility from water to protein, with stronger interactions correlating to greater protein flexibility and slower hydration water diffusion.

Published by the American Physical Society
2024
Iterative site percolation on triangular lattice
Authors: Li Ming , Deng Youjin
Published: September 2024

The site percolation on the triangular lattice stands out as one of the few exactly solved statistical systems. By initially configuring critical percolation clusters of this model and randomly reassigning the color of each percolation cluster, we obtain coarse-grained configurations by merging adjacent clusters that share the same color. It is shown that the process can be infinitely iterated in the infinite-lattice limit, leading to an iterative site percolation model. We conjecture from the self-matching argument that percolation clusters remain fractal for any finite generation, which can even take any positive real number by a generalized process. Extensive simulations are performed, and, from the generation-dependent fractal dimension, a continuous family of previously unknown universalities is revealed.

Published by the American Physical Society
2024
Measuring Irreversibility from Learned Representations of Biological Patterns
Authors: Li Junang , Liu Chih-Wei Joshua , Szurek Michal , Fakhri Nikta
Published: September 2024

Thermodynamic irreversibility is a fundamental characteristic of living matter, crucial for maintaining the complex spatiotemporal structures and functions that define biological systems. However, accurately quantifying biologically relevant irreversibility remains challenging due to noise and nonlinear interactions among many degrees of freedom. Here, we employ deep learning techniques to identify tractable, low-dimensional representations of phase-field patterns in a canonical protein signaling process—the Rho-GTPase system—as well as in complex Ginzburg-Landau dynamics. We demonstrate that factorizing variational autoencoder neural networks can robustly extract informative pattern features despite noise. These neural-network-derived representations reveal signatures of mesoscopic broken detailed balance and time-reversal asymmetry in both Rho-GTPase and complex Ginzburg-Landau wave dynamics. By applying the compression-based Ziv-Merhav estimator to these representations, we successfully recover irreversibility trends across complex Ginzburg-Landau patterns, which vary widely in spatiotemporal frequency and noise level. Our irreversibility estimates also recapitulate cell-activity trends in Rho-GTPase patterns subjected to metabolic inhibition. Furthermore, our framework distinguishes between stable and chaotic dynamical phases in these nonlinear systems. By leveraging advances in deep learning, our approach provides robust, model-free measurements of nonequilibrium and nonlinear behavior in complex living processes.

Published by the American Physical Society
2024
Reducing Leakage of Single-Qubit Gates for Superconducting Quantum Processors Using Analytical Control Pulse Envelopes
Authors: Hyyppä Eric , Vepsäläinen Antti , Papič Miha , Chan Chun Fai , Inel Sinan , Landra Alessandro , Liu Wei , Luus Jürgen , Marxer Fabian , Ockeloen-Korppi Caspar , Orbell Sebastian , Tarasinski Brian , Heinsoo Johannes
Published: September 2024

Improving the speed and fidelity of quantum logic gates is essential to reach quantum advantage with future quantum computers. However, fast logic gates lead to increased leakage errors in superconducting quantum processors based on qubits with low anharmonicity, such as transmons. To reduce leakage errors, we propose and experimentally demonstrate two new analytical methods, Fourier ansatz spectrum tuning derivative removal by adiabatic gate (FAST DRAG) and higher-derivative (HD) DRAG, both of which enable shaping single-qubit control pulses in the frequency domain to achieve stronger suppression of leakage transitions compared to previously demonstrated pulse shapes. Using the new methods to suppress the ef transition of a transmon qubit with an anharmonicity of −212 MHz, we implement RX(π/2) gates achieving a leakage error below 3.0×10−5 down to a gate duration of 6.25 ns without the need for iterative closed-loop optimization. The obtained leakage error represents a 20-fold reduction in leakage compared to a conventional cosine DRAG pulse. Employing the FAST DRAG method, we further achieve an error per gate of (1.56±0.07)×10−4 at a 7.9-ns gate duration, outperforming conventional pulse shapes both in terms of error and gate speed. Furthermore, we study error-amplifying measurements for the characterization of temporal microwave control-pulse distortions, and demonstrate that non-Markovian coherent errors caused by such distortions may be a significant source of error for sub-10-ns single-qubit gates unless corrected using predistortion.

Published by the American Physical Society
2024
The impact of social network and resource endowment of smallholders on sustainable apple production
Authors: Cui Shilei , Pathera Donasius , Li Yajuan , Jiao Xiaoqiang
Published: September 2024

Purpose

Smallholders are essential in ensuring food security; however, smallholder-dominated food production often involves high resource-environmental costs. This study analyzed the factors that differentiate horticultural practices, willingness to adopt technology and social networks between optimized practices (OPT) and farmer practices (FP) to provide localized and systematic solutions for the sustainable apple production.

Design/methodology/approach

To explore the approach of smallholder-dominated sustainable apple production, 257 apple producers in the Bohai Bay region, a major apple planting area in China, were investigated. Life cycle assessment (LCA), emergy analysis and social network analysis methods were used for evaluation.

Findings

The results showed that the net economic profit and emergy sustainability index (ESI) in OPT was 15.8 × 104 RMB·ha-1 and 1.2, respectively, which were 126.9 and 128.0% higher than FP. In contrast, greenhouse gas (GHG) emissions under OPT was 29.3% lower than those under FP. OPT has a higher percentage of adoption of scientific fertilizer application and water-saving irrigation technologies compared to FP. OPT has strong learning abilities, more social resources (such as technical training and sharing technical experience with others) and connections with stakeholders in the apple supply chain. Optimizing smallholders' social capital, willingness to adopt technology, behavioral willingness and technological awareness can promote sustainable apple production.

Originality/value

Considering the horticultural practices employed by smallholders in conjunction with their social networks, these factors contributed to the transition of smallholder-led apple production toward sustainability. The findings provided viable options and a theoretical basis for smallholder-dominated crop production to move toward sustainability, with significant implications for policymakers.
Do children study longer depending on their parents’ level of engagement? An analysis of factors related to Brazilian students’ engagement
Authors: Macana Esmeralda Correa , Mirolli Thamires Zaboto , Silva Ana Luíza Farage , Lazaretti Lauana Rossetto , Bianchi Lorenzo Luiz , Frio Gustavo Saraiva , França Marco Tulio Aniceto
Published: September 2024

Purpose

The purpose of this article is to investigate factors related to the time students spent on remote activities during the coronavirus (COVID-19) pandemic in 2020. Specifically, it analyzes whether the school’s relationship with the family and the guardians’ support are associated with longer study times for children and youth.

Design/methodology/approach

This was performed using an ordered logit model on data from two waves of the survey Remote Education in the Perspective of Students and Their Families (PENP) with a nationally and regionally representative sample of Brazilian public school students.

Findings

Results show the importance of contact between the school and the family and, to a greater extent, the direct support of parents or guardians. The odds of learners spending more hours studying increase 36% when schools provide guidance for parents and guardians; in turn, when they provide support for students during activities, these odds increase 144%.

Originality/value

Moreover, students spend more time doing school activities in the later years of elementary school, high school and when they attend a state school.
Mentoring research projects in the Croatian higher education document framework
Authors: Kušević Barbara
Published: September 2024

Purpose

Approaching mentoring from the theoretical tradition of continental pedagogy and contrasting it to the neoliberal organization of the academy, this paper aims to analyze how the Croatian higher education document framework constructs mentoring graduate and postgraduate students' research projects.

Design/methodology/approach

The analysis of 50 national- and university-level documents, which were coded using an adapted strategy described by Saldaña (2014), was guided by the following research questions. 1. Which elements of the mentor’s activity in guiding the research projects of graduate and postgraduate students are addressed by the relevant Croatian higher education documents? 2. Which elements of the graduate and postgraduate students’ activity in conducting research projects are addressed? 3. Which structural dimensions of mentoring these research projects are addressed?

Findings

The results point to the construction of mentoring as a pedagogical relationship based on guidance, support and dialog and also signal the processes of quantification of education and responsibilization of individuals.

Practical implications

The results can be used in the critical revision of the documents as well as in supporting mentors in their professional roles.

Originality/value

This is the first analysis of the Croatian higher education document framework focused on mentoring students’ research projects.
Antecedents of effectuation and causation in SMEs from emerging markets: the role of CEO temporal focus
Authors: Kozachenko Ekaterina , Shirokova Galina , Bodolica Virginia
Published: September 2024

Purpose

Previous studies considered effectuation and causation as alternative decision-making strategies used by entrepreneurs to navigate uncertainty, having various individual- and firm-level antecedents. This study aims to broaden our understanding of individual-level antecedents by examining the role of Chief Executive Officer (CEO) temporal focus in decision-making processes in small and medium-sized enterprises (SMEs).

Design/methodology/approach

Based on a multiple case study research design, the authors empirically analyse 16 Russian SMEs to uncover how the CEO temporal focus relates to the choice of effectuation/causation strategies under uncertainty.

Findings

CEOs with past orientation tend to adopt causation, future-oriented CEOs adhere to effectuation, while present-focused CEOs rely on both decision-making strategies (i.e. ambidexterity). Prior crisis-related experience is the underlying mechanism behind the relationship between CEO temporal orientation and effectuation/causation strategies. The authors formulate several propositions that may be tested in future studies in the field.

Originality/value

The contribution of this study consists in uncovering a new individual-level antecedent of effectuation/causation under uncertainty (i.e. CEO temporal focus) and suggesting that prior crisis experience acts as a mechanism underlying this relationship. The authors advance the strategic leadership theory by underscoring the CEO’s role in decision-making processes in SMEs.
Impact of digital financial inclusion on economic growth: a study on Bangladesh
Authors: Rahman Syed Mohammad Khaled , Chowdhury Mohammad Ashraful Ferdous , Sristi Nabila Rezwana
Published: September 2024

Purpose

The purpose of the study is to find out the impact of Digital Financial Inclusion (DFI) on economic growth [(Industrial Production Index (INDP)] of Bangladesh.

Design/methodology/approach

Using the monthly data over the period 2018 M12 to 2021 M12, this study applied the Auto-regressive Distributed Lag (ARDL) model to assess the effect of DFI indicators on INDP. The secondary data was collected from the Bangladesh Bank and CEIC Global Economic Data.

Findings

The study found that the majority of DFI indicators are positively associated with INDP. From the short-run ARDL, it is seen that one unit positive increase in Point of Sales Transactions (POST) can increase the INDP by 0.055 units. From the long-run ARDL, it is seen that POST and e-commerce transactions (ECOMT) have a significant positive impact, while Automated Teller Machine Transactions (ATMT) have a significant negative effect on INDP. One unit increase in POST and ECOMT increases INDP by 0.13544 and 0.11611 units, respectively.

Research limitations/implications

During the era of the fourth industrial revolution, the findings will be beneficial for policymakers, financial technology service providers, manufacturers, consumers, corporations and investors as they pave the way for a more inclusive approach to financial transactions for economic growth.

Originality/value

The study’s novelty is that it explored the influential DFI indicators and shed light on both short-run and long-run relationships between the indicators and macro-economy from the context of a developing nation.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-04-2023-0306
Gender perceptions of generative AI in higher education
Authors: Al-Samarraie Hosam , Sarsam Samer Muthana , Ibrahim Alzahrani Ahmed , Chatterjee Arunangsu , Swinnerton Bronwen J.
Published: September 2024

Purpose

This study explored the themes and sentiments of online learners regarding the use of Generative Artificial Intelligence (AI) or “generative AI” technology in higher education.

Design/methodology/approach

English-language tweets were subjected to topic modelling and sentiment analysis. Three prevalent themes were identified and discussed: curriculum development opportunities, lifelong learning prospects and challenges associated with generative AI use.

Findings

The results also indicated a range of topics and emotions towards generative AI in education, which were predominantly positive but also varied across male and female users.

Originality/value

The findings provide insights for educators, policymakers and researchers on the opportunities and challenges associated with the integration of generative AI in educational settings. This includes the importance of identifying AI-supported learning and teaching practices that align with gender-specific preferences to offer a more inclusive and tailored approach to learning.
Hedge fund activism and corporate litigation: an analysis of securities and non-securities lawsuits
Authors: Lim Yuree
Published: September 2024

Purpose

This study examines how corporate litigation, both securities-related and not, is affected by hedge fund (HF) activism.

Design/methodology/approach

We use a difference-in-differences (DiD) method, along with propensity score matching and firm fixed effects and a comparison of HF and non-HF activists for identification.

Findings

We find that companies that are targeted by HFs face operation-related lawsuits, mainly from stakeholders or competitors. This effect does not seem to be caused by targets' higher tendency to settle the cases. Our evidence shows that HF activists increase firm value for the target firms that are prone to litigation.

Originality/value

Therefore, our evidence supports the idea that the higher operation litigation risks are unintended consequences of improving firm efficiency through cost savings or restructuring of target firms by the activists.
Hospitalisations for non‐specific low back pain in people presenting to South Australian public hospital emergency departments
Authors: Orlando Joseph F , Burke Anne LJ , Beard Matthew , Guerin Michelle , Kumar Saravana
Published: September 2024

Objective

The present study sought to investigate predictors of hospitalisation in adults diagnosed with non‐specific low back pain (LBP) and/or sciatica from an ED.

Methods

A 5‐year, multicentre retrospective observational study was conducted across six public hospitals (metropolitan and regional) using data from electronic medical records. Patient presentations were identified using LBP diagnostic codes and key data extracted (patient demographics, clinical activity, discharge destination). Descriptive statistics and logistic regression were used to measure associations between identified variables and hospitalisation.

Results

There were 11 709 ED presentations across the study period. People aged ≥65 years (odds ratio [OR] 2.84, 95% confidence interval [CI] 2.61–3.10) and those who arrived at the ED via ambulance (age‐adjusted OR 2.68, 95% CI 2.44–2.95) were more likely to be hospitalised. People were also more likely to be hospitalised when triaged as more urgent, when blood tests or advanced spinal imaging were ordered, and when i.v./subcutaneous opioids or oral benzodiazepines were administered. Hospitalisation rates for LBP were lower in regional hospitals, in people residing in lower socioeconomic areas and in Indigenous Australians.

Conclusion

Certain patient characteristics and ED clinical activity are associated with hospitalisations for LBP. Understanding these factors will better inform the design and delivery of appropriate high‐quality care.
Evolution and modeling of texture changes and drying kinetics of bamboo shoots under high‐humidity air‐impingement blanching
Authors: Dai Jian‐Wu , Huang Jie , Zhou Hou‐Bin , Zhang Qing , Xu Li‐Jia , Liu Shu‐Xiang , Liu Yao‐Wen , Yin Peng‐Fei , Li Ying‐Lu , Qin Wen
Published: September 2024

This study investigated the effect of hot water blanching (HWB), high‐humidity air‐impingement blanching (HHAIB), different HHAIB blanching times (2, 4, 6, 8, and 10 min), and different HHAIB blanching temperatures (80, 85, 90, and 95°C) on texture quality, lignin content, weight loss, color, microstructure, and drying kinetics of bamboo shoots. After HWB treatment, the lignin content of bamboo shoots was apparently lower than that of HHAIB and the samples obtained the highest weight loss value of 6.13%. Both the texture values (brittleness and chewiness) and lignin content of bamboo shoots exhibited an overall downward trend as the HHAIB blanching time and blanching temperature increased. Specifically, the lignin content of bamboo shoots decreased from 5.59% to 4.58% with an increase in HHAIB blanching time from 2 to 10 min and dropped from 5.48% to 4.63% as HHAIB blanching temperature increased from 80 to 85°C, respectively. The lignin content was proved to be positively correlated (p < 0.05) with texture attributes (brittleness and chewiness). A second polynomial model was obtained for fitting the variation kinetics of lignin content during thermal processing. Reducing the HHAIB blanching time and blanching temperature would obtain a lower weight loss and a better color performance (ΔE and L*). Additionally, microstructure observation revealed that the distribution density of microchannels initially increased and then decreased with the extension of blanching time, while it continuously became firmer as HHAIB blanching temperature increased. Overall, the optimal processing parameters were achieved under the HHAIB blanching temperature of 85°C for 6 min, ensuring a high‐quality performance of bamboo shoot products.
Molecular and physiological mechanisms of aging are distinct in the cardiac right and left ventricles
Authors: McNair Benjamin D. , Yusifov Aykhan , Thornburg Joshua P. , Hoopes Caleb R. , Satyanarayana Sushumna B. , Roy Tathagato , Gigley Jason P. , Bruns Danielle R.
Published: September 2024

Aging is the primary risk factor for heart disease, the leading global cause of death. Right ventricular (RV) function predicts survival in several age‐related clinical contexts, yet no therapies directly improve RV function, in large part due to a poor mechanistic understanding of RV aging and how it is distinct from the widely studied left ventricle (LV). To address this gap, we comprehensively quantified RV functional and morphological remodeling with age. We further aimed to identify molecular mechanisms of RV aging thus we performed RNAseq on RV and LV from male and female young (4 months) and aged (19–21 months) C57BL6 mice. Contrary to the concentric hypertrophic remodeling and diastolic dysfunction that occurs in the LV, the aging RV underwent eccentric remodeling with significant dilation and impaired systolic function. Transcriptomic data were also consistent with ventricle‐specific aging, with few genes (13%) similarly shared between ventricles with aging. KEGG analysis identified shared aging genes in inflammatory and immune cell pathways that were confirmed by flow cytometry that demonstrated higher percent of GR1+ myeloid cells in both ventricles. Unique RV aging genes enriched in the biosynthesis of saturated fatty acids, PPAR signaling, and butanoate metabolism, and we identified putative novel RV‐specific aging genes. Together, we suggest that the RV and LV are unique cardiac chambers that undergo distinct remodeling with age. These robust differences may explain why therapies designed from LV‐based studies fail to improve RV function and suggest that future efforts emphasizing ventricular differences may elucidate new therapies for healthy cardiac aging.
Identification of oxidative stress biomarkers in apical periodontitis: A scoping review with bibliometric analysis
Authors: Macedo Signorelli Nara Sarmento , Rende Sávio Gabriel Silva , Iorio Eugenio Luigi , Ferraz Danilo Cassiano , Paranhos Luiz Renato , Moura Camilla Christian Gomes
Published: September 2024

Oxidative stress (OS) is a ubiquitous process for protecting against microorganisms' challenges. This review maps the most used methods for obtaining samples and analysing reactive oxygen species levels in apical periodontitis, following the PRISMA Extension for Scoping Reviews and is registered in Open Science Framework ([https://doi.org/10.17605/OSF.IO/D5U76]). A systematic search was conducted in electronic databases MEDLINE (PubMed), Embase, Scopus, Web of Science, LILACS, SciElo, OATD and DANS up to 17 July 2023. A total of 18 studies were included, with periapical tissue being the most common sample. Twenty‐eight different oxidative stress markers were identified, with inducible nitric oxide synthase being the most prevalent. The use of diverse biomarkers for oxidative stress assessment lacks specificity in identifying particular OS species for evaluating apical periodontitis and potential systemic effects. Studies are necessary to compare results obtained from less invasive methods (such as saliva and crevicular fluid) with those from periapical lesion samples.
Manifested U‐Waves Prior to Seizure Attacks in a Patient Who Had Remote Subarachnoid Hemorrhage: A Case Report
Authors: Kaneko Nao , Watanabe Masao , Mori Shusuke , Turker Isik , Okamoto Ken , Urabe Takao , Ai Tomohiko
Published: September 2024

Sudden unexpected death in epilepsy (SUDEP) refers to unpredictable demise of a person following a seizure. Electroencephalograms can directly measure electrical activity in the brain; however, it cannot predict when seizures will occur. The use of electrocardiograms (ECGs) to monitor changes in brain electrical activity has gained attention, recently. In this case report, we retrospectively reviewed ECGs taken before and after seizure activity in a 75‐year‐old male who had a remote subarachnoid hemorrhage. Interestingly, U‐waves appeared prior to his seizures and disappeared afterward, which suggests ECGs can be used to predict epilepsy in a certain population.
On the connectedness of stock returns and exchange rates in emerging and frontier markets in Africa
Authors: Atipaga Umar‐Farouk , Alagidede Imhotep , Tweneboah George
Published: September 2024

The effect of currency volatility on investments in Africa continues to dominate the headlines, especially in the recent period of global crisis and heightened geopolitical tensions. This paper tackles the dynamic relationship between stock returns and exchange rates in nine emerging and frontier African markets. The study departs from the usual VAR and GARCH models and employs a tool that accounts for time–frequency co‐movements and lead/lag relationships between exchange rates and stock returns in Africa. The bivariate wavelet technique applied to daily data from 1 April 2013 to 31 March 2022 established a profound negative co‐movement between stock returns and exchange rates, especially in the medium to long‐term frequencies. With exchange rates dominantly playing a leading role, it presents a case for policy consideration toward currency stability. We employed the partial wavelet approach to determine how stock returns and exchange rates related during the peak period of the COVID‐19 pandemic and found negative co‐movements within the short‐term frequency, revealing that investors preferred the short‐term horizon in times of crisis. However, when the covariate (COVID‐19) was controlled or suppressed, we discovered the health pandemic failed to drive both stock returns and exchange rates.