bluuebunny/crossref_metadata_2025 huggingface dataset:
Learning Programming With Augmented Reality‐Based Editor: A Dynamic Code Visualisation Approach
Authors: Aydin Merve , Çakiroğlu Ünal
Published: November 2024

Background

Students experience higher‐order thinking skills by finding ways to solve the problem, debugging errors while applying the solution, and testing the solution in programming. However, the inability to create schemas that will characterise programming structures is one of the difficulties during this process.

Objectives

This study aimed to create an augmented reality‐based programming editor and evaluate its contributions to learning programming. Text‐based programming codes developed by the students on the editor were instantly visualised through a traffic metaphor in dynamic visualisation via augmented reality. The findings of this study highlight the significance of a novel usage of augmented reality in shaping cognitive processes during the programming learning process.

Methods

An exploratory case study was adopted in the study. Participants voluntarily selected 15 students in the same secondary school's 4th and 5th grades. The data to determine the programming performances were collected via a programming performance test and analysed with the rubric created by the authors. Interviews and screen recordings were employed to determine the factors that had a role in the programming learning process.

Results and Conclusions

The results indicated that teaching programming using the augmented reality‐based editor has positively contributed to learning programming. The editor's scenario, animation, and error display features incorporated with an authentic dynamic visualisation were remarkable in this contribution. The editor also contributed to reducing students' efforts to create schemas for programming by bringing the context closer to reality throughout the programming process.
BMP10 Knockdown Modulates Endothelial Cell Immunoreactivity by Inhibiting the HIF‐1α Pathway in the Sepsis‐Induced Myocardial Injury
Authors: Guan Huan , Fang Jingyun
Published: November 2024

Sepsis is a life‐threatening syndrome triggered by a cascade of dysregulated immune responses. Sepsis‐induced myocardial injury (SIMI) substantially impacts the survival time of septic patients. However, the molecular mechanisms underlying the pathology of SIMI remain unclear. Immune‐related differentially expressed genes in SIMI were identified through RNA sequencing and bioinformatics analysis. The expression levels of hub genes were detected using reverse transcription quantitative PCR. BMP10 was knocked down in the lipopolysaccharide‐induced mouse and cardiac microvascular endothelial cell (CMEC) models, and its functions were assessed by a series of in vitro and in vivo assays. Cell adhesion and HIF‐1 pathway‐associated protein expressions were measured by western blot. Fenbendazole‐d3 was used to investigate whether BMP10 influenced SIMI development by modulating the HIF‐1 pathway. Six key genes were screened, of which BMP10, HAMP, TRIM5, and MLANA were highly expressed, and PTPRN2 and AVP were lowly expressed. BMP10 knockdown ameliorated histopathological changes and inhibited apoptosis and CMEC immune infiltration in SIMI. BMP10 knockdown reduced inflammatory factor (IL‐6, MCP‐1, IFN‐β, and CCL11) levels and protein expressions of cell adhesion‐related molecules (VCAM‐1 and ICAM‐1). Mechanistically, the HIF‐1 pathway agonist, Fenbendazole‐d3, significantly reversed the inhibitory effects of BMP10 knockdown on SIMI in vitro, indicating that BMP10 knockdown impeded the development of SIMI by suppressing the HIF‐1α pathway. BMP10 knockdown blocks SIMI progression by inhibiting the HIF‐1α pathway, which provides a new potential therapeutic strategy for SIMI treatment.
Binding of Infectious Hypodermal and Haematopoietic Necrosis Virus‐Like Particles to Mannose Receptor Stimulates Antimicrobial Responses in Immune‐Related Tissues of Peneaus vannamei
Authors: Weerachatyanukul Wattana , Pooljun Chettupon , Chotwiwatthanakun Charoonroj , Jariyapong Pitchanee
Published: November 2024

Mannose receptor (MR) is a transmembrane protein and a type of pattern‐recognition receptor (PRR) that plays a critical role in the immunity of mammals and fish. In this study, we examined the role of MR in binding with infectious hypodermal and haematopoietic necrosis virus‐like particle (IHHN‐VLP) and the downstream immune pathway that it triggers in the shrimp Peneaus vannamei. Upon IHHN‐VLP challenge, transcripts of MR in P. vannamei (PvMR) increased significantly in all examined tissues, particularly those related to shrimp immunity, including hemocyte, hepatopancreas and gill tissues. Specifically, IHHN‐VLP bound to the 34‐kDa PvMR protein in shrimp‐tissue extracts. Immunohistochemistry results of hemocytes showed that PvMR was initially localised on the plasma membrane but later internalised and dispersed throughout the cytoplasm after IHHN‐VLP administration. Binding between IHHN‐VLP and PvMR also induced significant upregulation of genes for the antimicrobial peptides (AMPs) penaeidin 3 and crustin, presumably to protect the shrimp against the viral infection. However, knocking down PvMR resulted in down‐regulation of all immune‐related genes examined. Overall, as an immune‐related PRR, PvMR serves as a receptor for invading viruses, which then trigger the expression of AMPs. Strategic designs using PvMR could be developed to either block the interaction of native virus with the host cells or provoke its up‐regulation to enhance shrimp immunity, which could open up opportunities to fight against IHHNV infection in shrimp.
Assessment of future risk of agricultural crop production under climate and social changes scenarios: A case of the Solo River basin in Indonesia
Authors: Shrestha Badri Bhakta , Rasmy Mohamed , Ushiyama Tomoki , Acierto Ralph Allen , Kawamoto Takatoshi , Fujikane Masakazu , Shinya Takafumi , Kubota Keijiro
Published: November 2024

Understanding the impacts of climate change and conversion of paddy field areas in the future on agricultural production is an essential part of flood‐risk management. However, the quantitative impact of flood on agricultural crops in the far‐future under climate change, considering prospective changes in paddy area, is still not clearly understandable. This study thus focused on quantitative analysis of flood impact on rice crops under climate change using MRI‐AGCM climate model outputs for the past (1979–2002) and far‐future (2075–2098) periods for the Solo River basin in Indonesia. We developed a quantitative damage assessment method by coupling water and energy budget‐based rainfall‐runoff‐inundation model outputs and a depth‐duration‐damage flood loss model. We also analyzed land‐use and land cover changes to project future paddy areas. The future rice production in the study basin may decrease by 21% by 2048 and by 24.6% by 2076 compared with that in 2020, due to the conversion of paddy fields to other land cover classes. The average annual flood damage value of rice crops may increase in the future period (2075–2098) by 93.7% (average damage: 666.08 billion IDR) compared with that in the past period (1979–2002) (average damage: 343.7 billion IDR), due to climate change impacts alone.
Choice on the menu: Increasing meal choice for people living in residential aged care, a pilot study
Authors: Wheeler Mikaela , Abbey Karen L. , Capra Sandra M.
Published: November 2024

Background

For residents in residential aged care (RAC), opportunities to make decisions about their meals are often limited. Increasing choice for residents requires significant changes to be made to the foodservice system to deliver nutritionally adequate, timely and enjoyable meals to residents. The pilot project aimed to understand the effect of increasing choice in meals on residents, staff and the foodservice system.

Methods

A pragmatic action research approach was used to collaboratively design and evaluate an altered a foodservice system that increased choice, enabling residents to place their order at the mealtime and choose from a menu of seven hot meal options for lunch and dinner. Outcome measures were measured pre‐ and post‐implementation and included food waste, resident satisfaction and foodservice costs.

Results

Resident satisfaction measured on a 5‐point Likert scale improved between pre‐ (3.60 ± 1.09) and post‐ (4.57 ± 0.49) measurements, whereas production waste increased (pre—55g, post—90 g) and foodservice costs increased (pre—$9.20–$11.14 per resident per day, post—$11.01–$12.15 per resident per day). Compared to the standard cook serve meal, consumption of protein foods increased marginally (+5 g), vegetable consumption increased (+11 g) and carbohydrate consumption decreased (−38 g) for meals consumed from the intervention menu.

Conclusions

Increasing choice can have a positive impact of resident satisfaction; however, further work is needed to investigate how production waste and costs can be addressed.
Wild‐type transthyretin cardiac amyloidosis and aortic stenosis: Can carpal tunnel syndrome help distinguish the chicken from the egg?
Authors: Delbarre Marc‐Antoine , Chadha Gagan Deep , Annabi Mohamed‐Salah , Nouri Refaat , Zaroui Amira , Blanc‐Durand Paul , Rasolonirina Diana , Kharoubi Mounira , Bejan Ancuta , Galat Arnaut , Oghina Silvia , Pibarot Philippe , Tribouilloy Christophe , Damy Thibaud
Published: November 2024

Background

The frequent association between transthyretin wild‐type (TTRwt) cardiac amyloidosis (CA) and aortic stenosis (AS) suggests a bidirectional relationship: TTRwt‐CA could induce AS and vice versa. Systemic manifestations may highlight this interaction: systemic amyloidogenesis would lead to systemic symptoms, CA, and AS, whereas the myocardial stresses induced by degenerative AS might promote local amyloidogenesis without systemic symptoms. Carpal tunnel syndrome (CTS) is the most frequently reported extracardiac symptom. Through a comparison of TTRwt‐CA patients with and without CTS, we sought to determine whether CTS serves as a reliable indicator of systemic involvement and its impact on cardiac and valvular characteristics.

Methods and results

A total of 411 consecutive patients with TTRwt‐CA were included. CTS, present in 70.3%, was associated with a younger age (80 vs. 84 years, p < 0.001), more extracardiac symptoms, and advanced CA, with greater cardiac remodeling and a higher heart‐to‐mediastinum ratio (1.63 vs. 1.54; p = 0.012) compared to patients without CTS. AS was present in 21% and 31% of patients with and without CTS, respectively (p = 0.024). Except for AS, these associations remained significant after adjusting for confounding factors. In severe AS, patients with CTS exclusively exhibited low‐flow low‐gradient (LFLG) AS and less severe class of aortic valvular calcium score (5.6% vs. 60%; p = 0.006) compared to those without CTS.

Conclusion

Our findings suggest that CTS may delineate two phenotypes in TTRwt‐CA: a systemic phenotype associated with advanced CA and poorly calcified LFLG AS, and a cardiac phenotype characterized by less severe CA and a mixed pattern of highly calcified AS, suggesting disparate pathophysiologies.
Impact of aging on the fracture strength of 3D‐printed fixed implant prostheses: A comparative analysis of monolithic and bi‐layer with or without fiber‐reinforced composite frameworks
Authors: Moreira Cançado Renata , Sakuno Adilson , Floriani Franciele , Zandinejad Amirali , Saraceni Cintia Helena Coury , Giovani Elcio Magdalena , Mesquita Alfredo Mikail Melo
Published: November 2024

Purpose

This study aims to evaluate the fracture strength of three‐unit, implant‐supported fixed dental prostheses (FDPs) constructed from 3D‐printed resin. It compares structures with and without fiber‐reinforced composite (FRC) frameworks under conditions that mimic artificial aging.

Materials and Methods

Forty FDPs were fabricated and divided into two groups: monolithic (n = 20) and bi‐layer (n = 20). The monolithic group (MG) consisted entirely of FDPs made from 3D‐printed resin for permanent restorations, while the bi‐layer group (BG) featured FDPs with an FRC framework veneered with the same 3D‐printed resin. Each group was subdivided into two subgroups: one subjected to artificial aging (MTG, n = 10; BTG, n = 10), and the other served as the baseline control (n = 10). All subgroups underwent a mechanical bending test, applying a single load to failure using a universal testing machine.

Results

There was a statistically significant difference in fracture strength due to the presence of the FRC framework (p < 0.01). The framework became the FDP more resistant to load. The mean load to failure and standard deviations were as follows: MG 406.59N (±33.84), MTG 286.20N (±152.15), BG 1142N (±162.88), and BTG 945N (±211.52). Although no statistical differences in strength were observed between aged and nonaged subgroups, variations in failure patterns emerged, with the BG and BTG groups showing a predominance of failures compared to the MG.

Conclusions

The inclusion of an FRC framework significantly enhanced the fracture strength of the FDPs. While the aging protocol did not alter the strength, failures predominantly occurred in the 3D‐printed resin superstructure at the connectors. The highest rate of fractures occurred in the premolar connector.
N–3 Fatty Acid Supplementation in Mothers and Infants for Childhood Psychomotor and Cognitive Development: An Updated Systematic Review and Meta‐Analysis
Authors: Liu Yingyu , Zhong Lijun , Sun Zhouyang , Feng Yuan , Ding Qianlu , Zhang Yujian
Published: November 2024

Long‐chain n–3 polyunsaturated fatty acid (PUFA) consumption in maternal and infants has been positively associated with cognitive and visual development. Tails even meta‐analysis showed mixed results. To evaluate the effects of maternal and infant n–3 PUFA supplementation on childhood psychomotor and cognitive development, PubMed, Embase, the Cochrane Library, PsycINFO and clinicaltrials.gov were searched. Randomized controlled trials were included to evaluate the effect on child cognitive and psychomotor outcomes of n–3 PUFA supplementation in mothers or infants (age ≤ 2 years). Findings were pooled with mean differences (MD) with 95% confidence intervals (95% CIs). Heterogeneity was explored using I2 and subgroup analyses, stratified for maternal (pregnancy and/or lactation) and infant (preterm infant and term infant). We identified 47 articles, with 14 trials on mothers and 33 on infants. Pooled results showed that infants' mental development index (MDI) increased with n–3 PUFA supplementation (MD = 2.91, 95% CI: 1.32–4.51, I2 = 65.1%). Subgroup analysis of MDI also demonstrated a benefit in preterm infants (MD = 4.16, 95% CI: 1.40–6.93, I2 = 49.5%) and term infants (MD = 2.28, 95% CI: 0.27–4.29, I2 = 70.1%). No significant association was found in subgroup analyses of supplementation to mothers during pregnancy or lactation period. Supplementation did not increase the psychomotor development index (PDI) in the mother or infant group. Language composite score increased for infants whose mothers accepted supplementation in pregnancy or breastfeeding (MD = 8.57, 95% CI: 5.09–12.04, I2 = 70.2%). The cognitive composite score did not improve in any subgroup. Intelligence Quotient (IQ) increased in the infants' group with n–3 PUFA supplementation (MD = 2.54, 95% CI: 0.45–4.63, I2 = 66.0%). Furthermore, IQ in term infants also improved (MD = 2.91, 95% CI: 0.24–5.57, I2 = 69.2%). The funnel plot and Egger's test confirmed no publication bias in any endpoints. Supplementation with n–3 PUFA during pregnancy or breastfeeding in mothers has increased language abilities. Furthermore, direct supplementation in term infants can improve intelligence in later childhood. However, insufficient evidence supports the claim that supplementation improves cognitive abilities.
Genomic correlates of vascular plant reproductive complexity and the uniqueness of angiosperms
Authors: Leslie Andrew B. , Mander Luke
Published: November 2024

Whole genome duplication (WGD) likely plays an important role in plant macroevolution, and has been implicated in diversification rate shifts, structural innovations, and increased disparity. But the general effects of WGD are challenging to evaluate, in part due to the difficulty of directly comparing morphological patterns across disparate clades.

We explored relationships between WGD and the evolution of reproductive complexity across vascular plants using a metric based on the number of reproductive part types. We used multiple regression models to evaluate the relative importance of inferred WGD events, genome size, and a suite of additional variables relating to growth habit and reproductive biology in explaining part type complexity.

WGD was a consistent predictor of reproductive complexity only among angiosperms. Across vascular plants generally, reproductive biology, clade identity, and the presence of bisexual strobili (those that produce microsporangiate and megasporangiate organs) were better predictors of complexity.

Angiosperms are unique among vascular plants in combining frequent polyploidy with high‐reproductive complexity. Whether WGD is mechanistically linked to floral complexity is unclear, but we suggest widespread polyploidy and increased complexity were ultimately facilitated by the evolution of herbaceous growth habits in early angiosperms.
Xizang meadow degradation alters resource exchange ratio, network complexity, and biomass allocation tradeoff of arbuscular mycorrhizal symbiosis
Authors: Dong Qiang , Ren Shijie , Willing Claire Elizabeth , Adams Catharine Allyssa , Li Yaoming , Ji Baoming , Gao Cheng
Published: November 2024

The response of arbuscular mycorrhizal (AM) symbiosis to environmental fluctuations involves resource exchange between host plants and fungal partners, associations between different AM fungal taxa, and biomass allocation between AM fungal spore and hyphal structures; yet a systematic understanding of these responses to meadow degradation remains relatively unknown, particularly in Xizang alpine meadow.

Here, we approached this knowledge gap by labeling dual isotopes of air 13CO2 and soil 15NH4Cl, computing ecological networks of AM fungal communities, and quantifying AM fungal biomass allocation among spores, intra‐ and extraradical hyphae.

We found that the exchange ratio of photosynthate and nitrogen between plants and AM fungi increased with the increasing severity of meadow degradation, indicating greater dependence of host plants on this symbiosis for resource acquisition. Additionally, using 18S rRNA gene metabarcoding, we found that AM fungal co‐occurrence networks were more complex in more degraded meadows, supporting the stress gradient hypothesis. Meadow degradation also increased AM fungal biomass allocation toward traits associated with intra‐ and extraradical hyphae at the expense of spores.

Our findings suggest that an integrated consideration of resource exchange, ecological networks, and biomass allocation may be important for the restoration of degraded ecosystems.
Proteolysis of host DEAD‐box RNA helicase by potyviral proteases activates plant immunity
Authors: Jia Zhaoxing , Rui Penghuan , Fang Xinxin , Han Kelei , Yu Tianqi , Lu Yuwen , Zheng Hongying , Chen Jianping , Yan Fei , Wu Guanwei
Published: November 2024

The precise mechanisms by which plant viral proteases interact with and cleave host proteins, thereby participating in virus–host interactions, are not well understood. Potyviruses, the largest group of known plant‐infecting RNA viruses, are known to rely on the nuclear inclusion protease a (NIa‐Pro) for the processing of viral polyproteins.

Here, we demonstrate that the proteolytic activity of NIa‐Pro from potyvirus turnip mosaic virus (TuMV) is indispensable for inducing hypersensitive cell death in Nicotiana benthamiana. NIa‐Pro targets and degrades the host DEAD‐box protein 5 (DBP5) via a specific cleavage motif, which initiates host cell death. Both the silencing of DBP5 and the overexpression of NIa‐Pro lead to an increased frequency of stop codon readthrough, which could be potentially harmful to the host, as it may result in the production of aberrant proteins. Unlike the NIa‐Pro of most other potyviruses, the NIa‐Pro of tobacco etch virus can also degrade DBP5 and trigger cell death, in both pepper and N. benthamiana.

Furthermore, we discovered that the TuMV‐encoded nuclear inclusion b can counteract NIa‐Pro‐induced cell death by co‐opting DBP5.

These findings unveil hitherto uncharacterized roles for plant virus proteases in cleaving host proteins and highlight the role of host DBP5 in modulating plant immunity.
Past innovations and future possibilities in plant chromosome engineering
Authors: Liu Yang , Liu Qian , Yi Congyang , Liu Chang , Shi Qinghua , Wang Mian , Han Fangpu
Published: November 2024

Plant chromosome engineering has emerged as a pivotal tool in modern plant breeding, facilitating the transfer of desirable traits through the incorporation of alien chromosome fragments into plants. Here, we provide a comprehensive overview of the past achievements, current methodologies and future prospects of plant chromosome engineering. We begin by examining the successful integration of specific examples such as the incorporation of rye chromosome segments (e.g. the 1BL/1RS translocation), Dasypyrum villosum segments (e.g. the 6VS segment for powdery mildew resistance), Thinopyrum intermedium segments (e.g. rust resistance genes) and Thinopyrum elongatum segments (e.g. Fusarium head blight resistance genes). In addition to trait transfer, advancements in plant centromere engineering have opened new possibilities for chromosomal manipulation. This includes the development of plant minichromosomes via centromere‐mediated techniques, the generation of haploids through CENH3 gene editing, and the induction of aneuploidy using KaryoCreate. The advent of CRISPR/Cas technology has further revolutionized chromosome engineering, enabling large‐scale chromosomal rearrangements, such as inversions and translocations, as well as enabling targeted insertion of large DNA fragments and increasing genetic recombination frequency. These advancements have significantly expanded the toolkit for genetic improvement in plants, opening new horizons for the future of plant breeding.
A Ball Python Colour Morph Implicates MC1R in Melanophore–Xanthophore Distribution and Pattern Formation
Authors: Garcia‐Elfring Alan , Roffey Heather L. , Abergas Jaren M. , Wuyts Jurgen , Hendry Andrew P. , Tzika Athanasia C. , Barrett Rowan D. H.
Published: November 2024

Reptiles showcase an extensive array of skin colours and patterns, yet little is known about the genetics of reptile colouration. Here, we investigate the genetic basis of the Clown colour morph found in captive‐bred ball pythons (Python regius) to study skin pigmentation and patterning in snakes. We obtained samples by crowdsourcing shed skin from commercial breeders and hobbyists. We applied a case–control design, whole‐genome pool sequencing, variant annotation, histological analyses, and electron microscopy imaging. We identified a missense mutation in a transmembrane region of the melanocortin‐1 receptor (MC1R) associated with the Clown phenotype. In classic avian and mammalian model species, MC1R is known for controlling the type and amount of melanin produced. In contrast, our results suggest that MC1R signalling might play a key role in pattern formation in ball pythons, affecting xanthophore–melanophore distribution. This work highlights the varied functions of MC1R across different vertebrate lineages and promotes a novel model system to study reptile colouration.
Inclusion Management Practices as a Pathway to Enhance Organizational Resilience in Response to a Crisis: An Empirical Test in the Context of the COVID‐19 Pandemic
Authors: Li Yixuan , Song Yifan , Wang Mo , Wu Yanbin , Zhu X. Susan , Alonso Alexander
Published: November 2024

Organizations inevitably face various forms of disruptive events (e.g., external crises), and sustaining long‐term prosperity requires them to stay resilient when encountering unexpected adversity. Prior crisis management research predominantly relied on qualitative case studies to examine efforts after a crisis had occurred, treating the crisis as a “given” rather than a variable. The exceptionality of crisis situations and the ad hoc nature of crisis countermeasures largely limit current knowledge about how organizations may manage employees to remain in a preparative stance for disruptive events. Integrating the inclusion literature, crisis management research, and event system theory, we propose inclusion management practices as a viable pathway for organizations to develop resilience resources and capabilities prior to a crisis, allowing them to exhibit greater robustness and agility when a crisis arises. Such robustness and agility, in turn, enhance organizational performance thereafter. We further pinpoint the strength of a crisis event as an important contingency shaping the effects of pre‐crisis inclusion management practices on organizations’ resilient responses and thereby performance. We tested our hypotheses in the context of the COVID‐19 pandemic crisis using longitudinal manager‐report survey data (N = 884 workplaces). We found that workplaces that implemented more inclusion management practices before COVID‐19 were more robust and agile in response to the pandemic crisis. Agility (but not robustness), in turn, was positively related to organizational performance. In addition, the effect of inclusion management practices on agility was stronger for workplaces with greater COVID‐19 event strength.
How will we work to conduct research and revitalization with our Indigenous language and culture?
Authors: de la Cruz Abelardo
Published: November 2024

From the twentieth century to today, foreigners and mestizos have conducted research on Nahua culture and the Nahuatl language from an etic perspective. In this article, I discuss how Nahuas see the role of non‐Indigenous researchers studying our language and culture and what role we—Indigenous Mexican scholars—must undertake in field research to revitalize Nahuatl, our language. I also discuss immigration from rural places to the city, which causes linguistic displacement and identity change. Finally, I propose a new way of engaging in community research through scholarship. When Nahuas carry out a research project, we make a decision to explore and learn about our culture from an emic perspective through which we engage in the language revitalization. We emphasize linguistic documentation using our mother tongue and then disseminate the Indigenous knowledge in the academia and in our small towns.
CsLCD and CsDCD are involved in nitric oxide‐enhanced salt tolerance in cucumber seedlings
Authors: Li Ailing , Li Xuelian , Chen Xinfang , Pan Xuejuan , Wu Xuetong , Liao Weibiao
Published: November 2024

Nitric oxide (NO) and hydrogen sulphide (H2S) play important roles in plant growth, development and environmental adaptation. Currently, there is few information on the mechanism by which H2S may be involved in NO‐induced salt tolerance. In this study, cucumber was used to investigate the role of NO and H2S and their relationship under salt stress. The results showed that the H2S donor sodium hydrosulfide (NaHS) and the NO donor sodium nitroprusside (SNP) significantly promoted the growth of cucumber seedlings under salt stress. However, hypotaurine (HT, an H2S scavenger) inhibited the positive effects of SNP under salt stress. Meanwhile, SNP treatment significantly increased the content of endogenous H2S, the activity of H2S synthesis‐related enzymes LCD, DCD, and CAS, and the expression of H2S synthesis‐related genes (CsLCD and CsDCD). In addition, the salt tolerance of cucumber seedlings was largely eliminated after silencing the H2S synthesis‐related genes CsLCD/CsDCD, while overexpression of CsLCD/CsDCD significantly enhanced the salt tolerance. It was further found that SNP enhanced the salt tolerance of CsLCD/CsDCD overexpression lines, but it had no positive effect on the tolerance of CsLCD/CsDCD silencing lines. Therefore, NO might enhance salt tolerance in cucumber seedlings by upregulating the expression of H2S synthesis‐related gene CsLCD/CsDCD.
TaCCS1‐B expression modulates copper, enzymatic antioxidants and polyphenols contents and provides abiotic stress tolerance in transgenic Arabidopsis
Authors: Tyagi Shivi , Shumayla  , Singh Samar , Pandey Ashutosh , Upadhyay Santosh Kumar
Published: November 2024

Abiotic stress, including osmotic and salinity stress, significantly affects plant growth and productivity. Copper chaperone for superoxide dismutase (CCS) is essential for copper homeostasis and oxidative stress management. In this study, we investigated the role of the TaCCS1‐B gene of bread wheat in enhancing stress tolerance in yeast and transgenic Arabidopsis. Expression of TaCCS1‐B increased abiotic stress tolerance in recombinant yeast cells. Phenotypic analysis of Arabidopsis TaCCS1‐B expressing lines demonstrated that they exhibited significantly higher germination rates, increased root length and better growth under osmotic and salinity stress than wild type. Additionally, the transgenic lines exhibited higher copper accumulation and enhanced photosynthetic pigments and proline level, coupled with reduced hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) contents. They also showed higher enzymatic antioxidants' activities, indicating reduced oxidative stress in transgenic lines, resulting in reduced flavonoid content. Gene expression analysis indicated modulated expression of stress‐responsive genes in the transgenic lines under stress conditions. These findings suggested the role of TaCCS1‐B in enhancing stress tolerance by improving copper homeostasis and regulating key stress‐responsive genes. This study highlights the potential of TaCCS1‐B for the development of better stress resilience crops, which is critical for sustaining agricultural productivity for food security under adverse environmental conditions.
Lipid Droplets in Aquatic Animals: Diversity, Biogenesis, and Functional Implications
Authors: Zhu Si , Lv Zhimeng , Ai Qinghui , Li Chenghua
Published: November 2024

Amid the aquaculture boom, chemical contaminants, diseases, and improper nutrition persist as threats to the sustainability of aquaculture. The accumulation of lipid droplets in different tissues has emerged as a hallmark in aquatic animals exposed to these stressors. While abundant knowledge is available on lipid droplets in mammals, relatively little is known in aquatic animals. Recently, interest in lipid droplets has grown in parallel with the recognition that they are actively engaged in the regulation of stress responses, metabolic modulation, infections, and immune response in different aquatic animals. This review first outlines the diversity of lipid droplets protein in various aquatic animals and discusses the function of lipid droplets in maintaining cellular homeostasis by contacting other organelles. Subsequently, the mechanisms of lipid droplet biogenesis in response to various chemical contaminants are summarized. Additionally, we describe the complex roles of lipid droplets in the host‐pathogen dynamic and the link between excessive lipid droplets accumulation and unwanted metabolic diseases in several aquatic animals. Finally, the potential application of lipid droplets in aquaculture is presented. A better understanding of the dynamics and functions of lipid droplets will facilitate the development of lipid droplets‐based therapeutic strategies, thereby improving the sustainability of aquaculture.
Soil scalping and soil microbial filtrates effects on the restoration of temperate grasslands
Authors: Guevara‐Torres Diego R. , Zakrzewski Martha , Facelli José M.
Published: November 2024

Recent research has shown that plant–soil–microbial interactions play an important role in determining plant community composition. The restoration of former farmlands (old‐fields) to temperate grasslands dominated by native perennial graminoids is often challenging due to great extent to the soil legacies caused by farming, grazing, and the dominance of invasive species. However, little is known about the effect of restoration techniques on the soil microbial communities and how microbes could affect the establishment of native species. We conducted a glasshouse experiment using intact core soil samples from old‐fields that were subject, or not, to soil scalping and that received soil microbial filtrates from different soil origins. We assessed the effects of combining these techniques on the microbial community and the growth of the native Wallaby grass (Rytidosperma auriculatum). Soil scalping notably modified edaphic properties, plant biomass, and soil microbial communities. The inoculation of soil microbial filtrates from remnant grasslands in combination with soil scalping produced the highest Wallaby grass biomass. Despite the lack of significant effects of soil microbial filtrates on edaphic properties and microbial communities, we observed subtle differences in the composition of fungal communities that could be linked to the growth of Wallaby grass. Our results indicate that soil microbial filtrates can increase biomass production of native grasses if techniques like removing the topsoil address soil legacies first. This study increases our understanding of the factors driving vegetation succession and represents an opportunity to improve restoration techniques.
The economic costs of supply chain decoupling
Authors: Attinasi Maria‐Grazia , Boeckelmann Lukas , Meunier Baptiste
Published: November 2024

As countries and firms increasingly seek ways to strengthen the resilience of their supply chains, this paper studies the global economic costs of a decoupling of global supply chains along geopolitical lines as well as in strategic sectors. We explore not only the long‐run effects but also the short‐run costs stemming from rigid wages and low substitutability across factors of production and input goods. We find that, in terms of welfare losses, the costs of decoupling are roughly five times higher in the short‐run compared with the long‐run, while country losses are heterogeneous. A reshaping of global supply chains increases the level of consumer prices in most countries, as well as producer prices, especially for trade‐intensive manufacturing sectors. Global supply chain decoupling entails also a reallocation of labour across skill levels. Finally, global trade would decrease substantially, driven by lower trade in intermediate inputs and a higher reliance of countries on domestic production.
Photobiomodulation studies on diabetic wound healing: An insight into the inflammatory pathway in diabetic wound healing
Authors: Mgwenya Tintswalo N. , Abrahamse Heidi , Houreld Nicolette N.
Published: November 2024

Diabetes mellitus remains a global challenge to public health as it results in non‐healing chronic ulcers of the lower limb. These wounds are challenging to heal, and despite the different treatments available to improve healing, there is still a high rate of failure and relapse, often necessitating amputation. Chronic diabetic ulcers do not follow an orderly progression through the wound healing process and are associated with a persistent inflammatory state characterised by the accumulation of pro‐inflammatory macrophages, cytokines and proteases. Photobiomodulation has been successfully utilised in diabetic wound healing and involves illuminating wounds at specific wavelengths using predominantly light‐emitting diodes or lasers. Photobiomodulation induces wound healing through diminishing inflammation and oxidative stress, among others. Research into the application of photobiomodulation for wound healing is current and ongoing and has drawn the attention of many researchers in the healthcare sector. This review focuses on the inflammatory pathway in diabetic wound healing and the influence photobiomodulation has on this pathway using different wavelengths.
Revealing subterahertz atomic vibrations in quantum paraelectrics by surface-sensitive spintronic terahertz spectroscopy
Authors: Chu Zhaodong , Yang Junyi , Li Yan , Hwangbo Kyle , Wen Jianguo , Bielinski Ashley R. , Zhang Qi , Martinson Alex B. F. , Hruszkewycz Stephan O. , Fong Dillon D. , Xu Xiaodong , Norman Michael R. , Bhattacharya Anand , Wen Haidan
Published: November 2024

Understanding surface collective dynamics in quantum materials is crucial for advancing quantum technologies. For example, surface phonon modes in quantum paraelectrics are thought to be essential in facilitating interfacial superconductivity. However, detecting these modes, especially below 1 terahertz, is challenging because of limited sampling volumes and the need for high spectroscopic resolution. Here, we report surface soft transverse optical (TO1) phonon dynamics in KTaO
3
and SrTiO
3
by surface-sensitive spintronic terahertz spectroscopy that can sense the collective modes only a few nanometers deep from the surface. In KTaO
3
, the TO1 mode softens and sharpens with decreasing temperature, leveling off at 0.7 terahertz. In contrast, this mode in SrTiO
3
broadens substantially below the quantum paraelectric crossover and coincides with the hardening of a sub–milli–electron volt phonon mode related to the antiferrodistortive transition. These observations that deviate from their bulk properties may have implications for interfacial superconductivity and ferroelectricity. The developed technique opens opportunities for sensing low-energy surface collective excitations.
Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon
Authors: Liu Fei , Wang Shi-Hui , Cheewangkoon Ratchadawan , Zhao Rui-Lin
Published: November 2024

Horizontal gene transfer (HGT) in fungi is less understood despite its significance in prokaryotes. In this study, we systematically searched for HGT events in 829 representative fungal genomes. Using a combination of sequence similarity and phylogeny-based approaches, we detected 20,093 prokaryotic-derived transferred genes across 750 fungal genomes, via 8,815 distinct HGT events. Notably, our analysis revealed that eight lifestyle-related traits significantly influence HGT diversity in fungi. For instance, parasites exhibited the highest estimated number of HGT-acquired genes, followed by saprotrophs, with symbionts showing the lowest. HGT-acquired genes were predominantly associated with metabolism and cellular functions and underwent purifying selection. Moreover, horizontally transferred genes with introns have significantly higher expression levels compared to intron-lacking genes, suggesting a probable role of intron gains in the adaptation of HGT-acquired genes. Overall, our findings highlight the influence of lifestyle on HGT diversity in fungi and underscore the substantial contribution of HGT to fungal adaptation.

IMPORTANCE

This study sheds new light on the role of horizontal gene transfer (HGT) in fungi, an area that has remained relatively unexplored compared to its well-established prevalence in bacteria. By analyzing 829 fungal genomes, we identified over 20,000 genes that fungi acquired from prokaryotes, revealing the significant impact of HGT on fungal evolution. Our findings highlight that fungal lifestyle traits, such as being parasitic or saprotrophic, play a key role in determining the extent of HGT, with parasites showing the highest gene acquisition rates. We also uncovered unique patterns of HGT occurrence based on fungal morphology and reproduction. Importantly, genes with introns, which are more highly expressed, appear to play a crucial role in fungal adaptation. This research deepens our understanding of how HGT contributes to the metabolic diversity and ecological success of fungi, and it underscores the broader significance of gene transfer in shaping fungal evolution.
Complete genome sequence of
Mumia
sp. Pv 4-285 isolated from the rhizosphere of
Phyllostachys viridiglaucescens
(Carrière) Rivière & C. Rivière
Authors: Kachor Anna , Samborskyy Markiyan , Rebets Yuriy , Gromyko Oleksandr
Published: November 2024

Mumia
are one of the rarest representatives of phylum Actinomycetota with only four species known. Here, we report the complete genome sequence of
Mumia
sp. Pv 4-285 isolated from a rhizosphere sample of
Phyllostachys viridiglaucescens
. The genome consists of a 4,649,352 bp circular chromosome with 4,361 protein-coding genes.
The genome sequence of a non-capsular natural
Bacillus anthracis
strain of A.Br.001/002 canSNP group isolated from permafrost in Yakutia, Russia
Authors: Goncharova Yulia , Bakhteeva Irina , Mironova Raisa , Skryabin Yuriy , Kislichkina Angelina , Solomentseva Aleksandra , Timofeev Vitalii
Published: November 2024

We present the results of the whole-genome sequencing of a
Bacillus anthracis
strain isolated from a permafrost sample collected in Yakutia, Russia. This strain was named YakM12. Phylogenetic analysis showed that YakM12 belongs to the canSNP group A.Br.001/002 and is genetically close to the Sterne vaccine strain.
Comparative genomic analysis of ten
Elizabethkingia
anophelis
isolated from clinical patients in China
Authors: Wu Fei , Wu Yan , Zhang Miaomiao , Tian Lijun , Li Xue , Luo Xi , Zhang Yiquan , Lu Renfei
Published: November 2024

Elizabethkingia anophelis
is an emerging pathogen that causes life-threatening infections in neonates and immunocompromised patients. In this study, we performed next-generation sequencing (NGS) to characterize 10
E. anophelis
strains isolated from clinical patients in Nantong, China. Core, accessory, and unique genomes were composed of 2,891, 1,633, and 498 genes, respectively. Based on genetic screening for antimicrobial resistance genes (AMRs), all
E. anophelis
strains carried the same AMRs, including
bla
B
,
bla
CME
, and
bla
GOB
. The virulence factors (VFs) in the 10 strains were classified into 13 functional categories, and the differences between strains were mainly in immune modulation and nutritional/metabolic factor. We further analyzed the genomic features of one of ten strains, NT06 strain. The capsule type of NT06 was X, which is rare among
E. anophelis
strains. Based on comparative analyses, we first found that NT06 carried the YclNOPQ-like operon, which is the complete transporter for petrobactin, to acquire iron. The genomic features are important for further investigations of epidemiology, resistance, virulence, and to identify appropriate treatments.

IMPORTANCE

Elizabethkingia anophelis
strains are opportunistic pathogens causing meningitis, bloodstream infections, and endophthalmitis in vulnerable populations. There is a lack of knowledge of the genetic diversity, presence of antimicrobial resistance genes (AMRs), and virulence factors (VFs) in
E. anophelis
isolated from clinical patient
s
in China. Based on next-generation sequencing (NGS) and comparative genomic analyses, we determined the genomic features, phylogeny, and diversity of
E. anophelis
strains isolated from patients and identified a large accessory genome, intrinsic AMRs, and variable VFs. Based on comparative analyses, we identified a key strain, NT06, that carried a unique capsule type of X and the siderophore-mediated iron acquisition system (
yclNOPQ
-like genes). These findings advance our understanding of the genomic plasticity, evolution, and pathogenicity determinants of
E. anophelis
.
Differential vasoproliferative traits of
Bartonella henselae
strains associated with autotransporter BafA variants
Authors: Kondo Yuka , Suzuki Masahiro , Sato Shingo , Maruyama Soichi , Sei Akiko , Ma Xingyan , Nakano Kota , Doi Yohei , Tsukamoto Kentaro
Published: November 2024

Bartonella henselae,
a Gram-negative facultative intracellular bacterium, is the etiological agent of cat-scratch disease and also causes bacillary angiomatosis in immunocompromised individuals. Although the ability to promote vascular endothelial cell proliferation differs among
Bartonella
species, variations among strains within
B. henselae
remain unclear.
Bartonella
angiogenic factor A (BafA) and
Bartonella
adhesin A (BadA) have been identified as autotransporters of
B. henselae
that are involved in endothelial cell proliferation. Although strain-specific differences in the expression of BadA and the VirB/D4 type IV secretion system have been reported, BafA expression among
B. henselae
strains has yet to be examined. Therefore, the present study investigated the proliferation-promoting ability of 13
B. henselae
strains from several sources in human umbilical vein endothelial cells (HUVECs). We identified BafA variants 1 and 2 based on the deduced amino acid sequences of its passenger domain. The recombinant proteins of both variants exhibited similar proliferation activity against HUVECs. However, BafA variant 2 strains showed cytotoxicity at a high bacterial inoculum in a direct coculture with HUVECs, which was attenuated in an indirect coculture. These strains, in contrast to BafA variant 1 strains, highly expressed BadA and exhibited bacterial aggregation. Based on a core genome SNP analysis of 50
B. henselae
strains, the BafA variant types corresponded to clades 1–4. These results indicate that vasoproliferative traits differ among
B. henselae
clades based on the variant types. Therefore, this study provides a new conceptual framework in which the clades of
B. henselae
may predict their pathogenicity in humans.

IMPORTANCE

Bartonella
species including
Bartonella henselae
,
Bartonella quintana
, and
Bartonella bacilliformis
cause vasoproliferative lesions. Their proliferation-promoting ability in vascular endothelial cells differs among
Bartonella
species; however, it is unclear whether these differences exist among
B. henselae
strains. We herein showed that
B. henselae
strains exhibited variable proliferation-promoting ability and cytotoxicity in vascular endothelial cells, which corresponded to the
bafA
gene variants possessed by the strains. The expression levels of
Bartonella
angiogenic factor A (BafA) and
Bartonella
adhesin A, as well as the degree of proliferation-promoting ability and cytotoxicity in endothelial cells, varied among the strains. A core genome SNP analysis of strains using whole genome sequencing data divided
B. henselae
strains into four clades, with each clade corresponding to BafA variants 1–4. These results suggest the differential vasoproliferative potency of
B. henselae
, with potential implications in clinical management, including risk stratification and predictions of the clinical course.