bluuebunny/crossref_metadata_2025 huggingface dataset:
Last-century vegetation dynamics in a highland Pyrenean national park and implications for conservation
Authors: Rull V. , Blasco A. , Sigró J. , Vegas-Vilarrúbia T.
Published: March 2024

Ecological records from before and after the creation of natural parks are valuable for informing conservation and restoration actions. Such records are often unavailable, but high-resolution paleoecological studies may provide useful information. This paper presents a sub-decadal paleoecological reconstruction of vegetation and landscape in a national park in the Pyrenean highlands, established in the 1950s. The park lands were traditionally been used for small-scale cultivation, extensive grazing, forest exploitation and, since 1910, hydroelectricity generation following the damming of numerous glacial lakes. A significant finding is that present-like forests, with negligible changes in composition, have dominated the landscape during the study period. Major vegetation changes involved shifts in forest cover, influenced by both climatic and anthropic factors. Interestingly, the creation of the park in 1955 and the initial restrictions on forest exploitation in 1975 did not significantly affect vegetation cover or composition. Forest expansion did not occur significantly until the 1980s when the park was enlarged, and forest exploitation was further restricted. This expansion peaked in the mid-1990s coinciding with a warming trend and a decrease in fire incidence, before declining due to warmer and drier climates. This decline in forest cover occurred concurrently with the ongoing global forest dieback phenomenon and may be exacerbated by the predicted global warming in this century, which could also increase fire incidence due to the accumulation of dead wood. Under current conservation measures, the main threats are global warming, fire and, on a more local scale, the massification of tourism. Expanding the park and implementing forest restoration actions on degraded terrains surrounding the park could only be beneficial.
Dorsal CA1 silencing degrades tactile short-term memory
Authors: Someck Shirly , Katz Netta , Levi Amir , Stark Eran
Published: March 2024

Previous studies in rodents showed that the hippocampus is involved in spatial short-term memory (STM), but hippocampal necessity for maintaining short-term sensory memories is unknown. Here, we develop tactile discrimination and STM tasks for freely-moving mice. Subjects learn to discriminate between textures after four shaping sessions and a single post-shaping session, and learn the STM task within a dozen sessions. Transient closed-loop silencing of dorsal hippocampal region CA1 during memory maintenance degrades task performance, compared to interleaved control blocks. Thus, uninterrupted hippocampal activity is required for acting upon tactile information maintained in STM. The findings suggest that the role of the hippocampus extends beyond spatial navigation, encoding memories, and long-term consolidation of experiences.
Thermal Characterization and Preclinical Validation of an Accessible, Carbon Dioxide-Based Cryotherapy System
Authors: Hu Yixin , Gordon Naomi , Ogg Katherine , Kraitchman Dara L. , Durr Nicholas J. , Surtees Bailey
Published: March 2024

To investigate the potential of an affordable cryotherapy device for accessible treatment of breast cancer, the performance of a novel carbon dioxide-based device was evaluated through both benchtop and in vivo canine models. This novel device was quantitatively compared to a commercial device that utilizes argon gas as the cryogen. The thermal behavior of each device was characterized through calorimetry and by measuring the temperature profiles of iceballs generated in tissue phantoms. A 45-minute treatment from the carbon dioxide device in a tissue phantom produced a 1.67 ± 0.06 cm diameter lethal isotherm that was equivalent to a 7-minute treatment from the commercial argon-based device which produced a 1.53 ± 0.15 cm diameter lethal isotherm. In vivo validation was performed with the carbon dioxide-based device in one spontaneously occurring canine mammary mass with two standard 10-minutes freezes. Following cryotherapy, this mass was surgically resected and analyzed for necrosis margins via histopathology. The histopathology margin of necrosis from the in vivo treatment with the carbon dioxide device at 14 days post cryoablation was 1.57 cm. While carbon dioxide gas has historically been considered an impractical cryogen due to its low working pressure and high boiling point, this study shows that carbon dioxide-based cryotherapy may be equivalent to conventional argon-based cryotherapy in the size of the ablation zone in a standard treatment time. The validation of the carbon dioxide device performed in this study is an important step towards bringing accessible breast cancer treatment to women in low-resource settings.
Human brain aging heterogeneity observed from multi-region omics data reveals a subtype closely related to Alzheimer’s disease
Authors: Peng Shouneng , Wang Erming , Wang Minghui , Wang Xusheng , Yu Kaiwen , Fu Yingxue , Poudel Suresh , Ho Lap , Narayan Sushma , Huffman Derek M. , Gaiteri Chris , Bennet David A. , Ehrlich Michelle E. , Haroutunian Vahram , Peng Junmin , Zhang Bin , Tu Zhidong
Published: March 2024

INTRODUCTION: The interconnection between brain aging and Alzheimer’s disease (AD) remain to be elucidated. METHODS: We investigated multi-omics (transcriptomics and proteomics) data from multiple brain regions (i.e., the hippocampus (HIPP), prefrontal cortex (PFC), and cerebellum (CRBL)) in cognitively normal individuals. RESULTS: We found that brain samples could be divided into ADL (AD-like) and NL (normal) subtypes which were correlated across brain regions. The differentially expressed genes in the ADL samples highly overlapped with AD gene signatures and the changes were consistent across brain regions (PFC and HIPP) in the multi-omics data. Intriguingly, the ADL subtype in PFC showed more differentially expressed genes than other brain regions, which could be explained by the baseline gene expression differences in the PFC NL samples. DISCUSSION: We conclude that brain aging heterogeneity widely exists, and our findings corroborate with the hypothesis that AD-related changes occur decades before the clinical manifestation of cognitive impairment in a sub-population.
Formamide denaturation of double-stranded DNA for fluorescencein situhybridization (FISH) distorts nanoscale chromatin structure
Authors: Shim Anne R. , Frederick Jane , Pujadas Emily M. , Kuo Tiffany , Ye I Chae , Pritchard Joshua A. , Dunton Cody L. , Gonzalez Paola Carrillo , Acosta Nicolas , Jain Surbhi , Anthony Nicholas M. , Almassalha Luay M. , Szleifer Igal , Backman Vadim
Published: March 2024

As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. Here, we investigate the effects of fluorescent labeling of DNA sequences within chromatin using the gold standard technique of three-dimensional fluorescencein situhybridization (3D FISH). The chemical reagents involved in the 3D FISH protocol, specifically formamide, cause significant alterations to the sub-200 nm (sub-Mbp) chromatin structure. Alternatively, two labeling methods that do not rely on formamide denaturation, resolution after single-strand exonuclease resection (RASER)-FISH and clustered regularly interspaced short palindromic repeats (CRISPR)-Sirius, had minimal impact on the three-dimensional organization of chromatin. We present a polymer physics-based analysis of these protocols with guidelines for their interpretation when assessing chromatin structure using currently available techniques.
Synthesis and Biological Assessment of Chalcone and Pyrazoline Derivatives as Novel Inhibitor for ELF3-MED23 Interaction
Authors: Hwang Soo-Yeon , Jeon Kyung-Hwa , Lee Hwa-Jong , Moon Inhye , Jung Sehyun , Kim Seul-Ah , Jo Hyunji , Park Seojeong , Ahn Misun , Kwak Soo-Yeon , Na Younghwa , Kwon Youngjoo
Published: March 2024

HER2 overexpression significantly contributes to the aggressive nature and recurrent patterns observed in various solid tumors, notably gastric cancers. Trastuzumab, HER2-targeting monoclonal antibody drug, has shown considerable clinical success, however, readily emerging drug resistance emphasizes the pressing need for improved interventions in HER2-overexpressing cancers. To address this, we proposed targeting the protein-protein interaction (PPI) between ELF3 and MED23 as an alternative therapeutic approach to trastuzumab. In this study, we synthesized a total of 26 compounds consisting of 10 chalcones, 7 pyrazoline acetyl, and 9 pyrazoline propionyl derivatives, and evaluated their biological activity as potential ELF3-MED23 PPI inhibitors. Upon systematic analysis, candidate compound10was selected due to its potency in downregulating reporter gene activity ofERBB2promoter confirmed by SEAP activity and its effect on HER2 protein and mRNA levels. Compound10effectively disrupted the binding interface between the ELF3 TAD domain and the 391-582 amino acid region of MED23, resulting in successful inhibition of the ELF3-MED23 PPI. This intervention led to a substantial reduction in HER2 levels and its downstream signals in the HER2-positive gastric cancer cell line. Subsequently, compound10induced significant apoptosis and anti-proliferative effects, demonstrating superiorin vitroandin vivoanticancer activity overall. We found that the anticancer activity of compound10was not only restricted to trastuzumab-sensitive cases, but was also valid for trastuzumab-refractory clones. This suggests its potential as a viable therapeutic option for trastuzumab-resistant gastric cancers. In summary, compound10could be a novel alternative therapeutic strategy for HER2-overexpressing cancers, overcoming the limitations of trastuzumab.
Coupling of saccade plans to endogenous attention during urgent choices
Authors: Goldstein Allison T , Stanford Terrence R , Salinas Emilio
Published: March 2024

The neural mechanisms that willfully direct attention to specific locations in space are closely related to those for generating targeting eye movements (saccades). However, the degree to which the voluntary deployment of attention to a location necessarily activates a corresponding saccade plan remains unclear. One problem is that attention and saccades are both automatically driven by salient sensory events; another is that the underlying processes unfold within tens of milliseconds only. Here, we use an urgent task design to resolve the evolution of a visuomotor choice on a moment-by-moment basis while independently controlling the endogenous (goal-driven) and exogenous (salience-driven) contributions to performance. Human participants saw a peripheral cue and, depending on its color, either looked at it (prosaccade) or looked at a diametrically opposite, uninformative non-cue (antisaccade). By varying the luminance of the stimuli, the exogenous contributions could be cleanly dissociated from the endogenous process guiding the choice over time. According to the measured timecourses, generating a correct antisaccade requires about 30 ms more processing time than generating a correct prosaccade based on the same perceptual signal. The results indicate that saccade plans elaborated during fixation are biased toward the location where attention is endogenously deployed, but the coupling is weak and can be willfully overridden very rapidly.
Evaluation of a Machine Learning-guided Strategy for Elevated Lipoprotein(a) Screening in Health Systems
Authors: Aminorroaya Arya , Dhingra Lovedeep S , Oikonomou Evangelos K , Khera Rohan
Published: March 2024

Background

While universal screening for Lp(a) is increasingly recommended, fewer than 0.5% of the patients undergo Lp(a) testing. Here, we assessed the feasibility of deploying Algorithmic Risk Inspection for Screening Elevated Lp(a) (ARISE), a validated machine learning tool, to health system EHRs to increase the yield of Lp(a) testing.

Methods

We randomly sampled 100,000 patients from the Yale-New Haven Health System (YNHHS) to evaluate the feasibility of ARISE deployment. We also evaluated Lp(a) tested populations in the YNHHS (N=7,981) and the Vanderbilt University Medical Center (VUMC) (N=10,635) to assess the association of ARISE score with elevated Lp(a). To compare the representativeness of the Lp(a) tested population, we included 456,815 participants from the UK Biobank and 23,280 from three US-based cohorts of ARIC, CARDIA, and MESA.

Results

Among 100,000 randomly selected YNHHS patients, 413 (0.4%) had undergone Lp(a) measurement. ARISE score could be computed for 31,586 patients based on existing data, identifying 2,376 (7.5%) patients with a high probability of elevated Lp(a). A positive ARISE score was associated with significantly higher odds of elevated Lp(a) in the YNHHS (OR 1.87, 95% CI, 1.65-2.12) and the VUMC (OR 1.41, 95% CI, 1.24-1.60). The Lp(a) tested population significantly differed from other study cohorts in terms of ARISE features.

Conclusions

We demonstrate the feasibility of deployment of ARISE in US health systems to define the risk of elevated Lp(a), enabling a high-yield testing strategy. We also confirm the very low adoption of Lp(a) testing, which is also being restricted to a highly selected population.
The Impact of Artificial Intelligence on Large Vessel Occlusion Stroke Detection and Management: A Systematic Review Meta-analysis
Authors: Zebrowitz Elan , Dadoo Sonali , Brabant Paige , Uddin Anaz , Aifuwa Esewi , Maraia Danielle , Ettienne Mill , Yakubov Neriy , Babu Myoungmee , Babu Benson
Published: March 2024

Introduction Stroke remains the second leading cause of death worldwide, with many survivors facing significant disabilities. In acute stroke care, the timeless adage 'Time is brain' underscores the vital need for quick action. Innovative Artificial Intelligence (AI) technology potentially offers swift detection and management of acute ischemic strokes, leading acute stroke care towards enhanced automation. Methods The study is registered with Prospero under CRD42024496716 and adheres to the Problem, Intervention, Comparison, and Outcomes framework (PICO). The analysis used Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We searched Embase, PubMed, DBLP, Google Scholar, IEEE Xplore, Cochrane database, IEEE, Web of Science, ArXiv, MedRxiv Web of Science, and Semantic Scholar. The articles included were published between 2019 and 2023. Out of 1,528 articles identified, thirty-eight met the inclusion criteria. Results We compared AI-augmented Large Vessel Occlusion (LVO) detection and non-AI in various patient processing times related to emergent endovascular therapy in acute ischemic strokes. Triage Time, Door-to-Intervention Notification Time (INR), and Door-to -Arterial Puncture Time revealed an odds ratio (OR) of 0.39 (95% CI: 0.29 - 0.54, p < 0.001), 0.30 30 (95% CI: 0.21 - 0.42, p < 0.001), and 0.50 (95% CI: 0.30 - 0.82, p = 0.007), respectively. CT-to-Puncture-Time and Door-to-CTA-Time yielded an OR of 0.57 (95% CI: 0.31 - 1.04, p = 0.065) and 0.77 (95% CI: 0.37-1.60, p = 0.489), respectively. The Last Known Well (LWK) to Time of Arrival resulted in an OR of 1.15 (95% CI: 0.83 - 1.59, p = 0.409). AI stroke detection sensitivity OR of 0.91 (95% CI: 0.88 - 0.95, p < 0.001), National Institute of Health score (NIHSS) 16.20 (95% CI: 14.96 - 17.45, p = 0.001). Patient Transfer-Times between primary and comprehensive stroke centers generated an OR of 0.98 (95% CI: 0.73 - 1.32, p = 893). Similarly, Door-in-Door-Out Time (DIDO) had an OR of 1.19 (95% CI: 0.21 - 6.88, p = 0.848). The results indicated significant differences across several parameters between the AI and non-AI groups. Conclusion Our findings highlight how AI augments healthcare providers' ability to detect and manage strokes swiftly and accurately within acute care settings. As these technologies advance and AI becomes more integrated into healthcare systems, longitudinal studies are critical in evaluating its impact on workflow efficiency, cost-effectiveness, and clinical outcomes.
A scoping review of fair machine learning techniques when using real-world data
Authors: Huang Yu , Guo Jingchuan , Chen Wei-Han , Lin Hsin-Yueh , Tang Huilin , Wang Fei , Xu Hua , Bian Jiang
Published: March 2024

Objective: The integration of artificial intelligence (AI) and machine learning (ML) in health care to aid clinical decisions is widespread. However, as AI and ML take important roles in health care, there are concerns about AI and ML associated fairness and bias. That is, an AI tool may have a disparate impact, with its benefits and drawbacks unevenly distributed across societal strata and subpopulations, potentially exacerbating existing health inequities. Thus, the objectives of this scoping review were to summarize existing literature and identify gaps in the topic of tackling algorithmic bias and optimizing fairness in AI/ML models using real-world data (RWD) in health care domains. Methods: We conducted a thorough review of techniques for assessing and optimizing AI/ML model fairness in health care when using RWD in health care domains. The focus lies on appraising different quantification metrics for accessing fairness, publicly accessible datasets for ML fairness research, and bias mitigation approaches. Results: We identified 11 papers that are focused on optimizing model fairness in health care applications. The current research on mitigating bias issues in RWD is limited, both in terms of disease variety and health care applications, as well as the accessibility of public datasets for ML fairness research. Existing studies often indicate positive outcomes when using pre-processing techniques to address algorithmic bias. There remain unresolved questions within the field that require further research, which includes pinpointing the root causes of bias in ML models, broadening fairness research in AI/ML with the use of RWD and exploring its implications in healthcare settings, and evaluating and addressing bias in multi-modal data. Conclusion: This paper provides useful reference material and insights to researchers regarding AI/ML fairness in real-world health care data and reveals the gaps in the field. Fair AI/ML in health care is a burgeoning field that requires a heightened research focus to cover diverse applications and different types of RWD.
Unveiling the Intricate Sinking behavior of Large Diatoms: Insights from Time-Frequency Analysis ofPalmerina hardmanianaSinking under Silicate-Depleted Conditions
Authors: Zhang Ping , Lu Jiachang , Li Lang , Zhuang Junlian , Lai Junxiang , Shi Tianying , Li Jie
Published: March 2024

Nutrient limits impact diatom sinking in time domain, but response in time-frequency domain is unclear. Studying the response of large diatoms to nutrients exclusively in the time domain fails to fully capture the complete impact of nutrient limitations on sinking behavior due to the absence of crucial information, including period and frequency. Wavelet analysis provides valuable insights into the period and frequency of signals and unveils their positions in the time. This study investigated the sinking behavior response of the large diatomPalmerina hardmanianato silicate-depleted conditions in the time-frequency domain using wavelet analysis. The results showed thatP. hardmanianawas capable of regulating its sinking speed, and this regulation occurred intermittently in time. The predominant frequency of intermittent regulation fell within the range of 0.13-0.50 Hz (equivalent to a period of 2-8 s) for both control and silicate-depleted conditions. The similarity in the frequency range of regulation between the two groups suggests the involvement of shared physiological mechanisms.P. hardmanianaresponded to silicate depletion by intensifying the regulation of 0.13-0.50 Hz, which was reflected in the time domain as a change in the proportion of different instantaneous sinking speeds and consequently lead to a significant increase or decrease in the mean sinking speed(p<0.05). Additionally, the regulation ofP. hardmanianasinking behavior was also influenced by the physiological state of the cells. Short-term silicate stress (30 min) enhanced the oscillation power of sinking regulation, while prolonged silicate stress (≥ 3 d) led to a decline in oscillation power.
Overexpression ofPpGL2fromPrunus persicaenhanced soybean drought tolerance
Authors: Wei Li , Li Zhao , Dahong Li , Hong-yan Li
Published: March 2024

The HD-ZIP transcription factor family plays crucial roles in plant growth and abiotic stress responses. While its diverse functions and regulatory mechanisms are well-documented, its role in conferring abiotic stress tolerance in peaches remains largely unexplored. Here, we report the bioinformatics profile of PpGL2, a member of the HD-ZIP transcription factor family, and its integration into the soybean genome to assess its potential impact on drought tolerance. Localization studies in onion cells revealed nuclear localization of PpGL2-GFP fusion protein, while yeast hybridization experiments demonstrated its transactivation and DNA binding abilities.PpGL2overexpression under drought conditions led to reduced accumulation of reactive oxygen species and malondialdehyde compared to wild-type, decreased water loss rate, and increased chlorophyll content and relative water content. Additionally,PpGL2overexpression promoted plant height and root length under drought stress, accompanied by altered transcription levels of stress-related genes across different plant genotypes. Furthermore,PpGL2overexpression enhanced oxidative tolerance. Therefore, our findings suggest thatPpGL2overexpression holds promise for enhancing soybean drought resistance, offering a novel approach to improving soybean drought resistance.
The flavohemoglobin Yhb1 is a new interacting partner of the heme transporter Str3
Authors: Lo Ying Ping Florie , Vahsen Tobias , Brault Ariane , Néré Raphaël , Labbé Simon
Published: March 2024

Nitric oxide (NO) is a gaseous molecule that induces nitrosative stress, which can jeopardize cell viability. Yeasts have evolved diverse detoxification mechanisms to effectively counteract NO-mediated toxicity. One mechanism relies on the flavohemoglobin Yhb1, whereas a second one requires the S-nitrosoglutathione reductase Fmd2. However, in this study, we eliminate any contribution from Fmd2 by using strains deleted for this gene. To investigate heme-dependent activation of Yhb1 in response to NO, we usehem1Δ-derivativeSchizosaccharomyces pombestrains lacking the initial enzyme in heme biosynthesis, forcing cells to assimilate heme from external sources. Under these conditions,yhb1+mRNA levels are repressed in the presence of iron through a mechanism involving the GATA-type transcriptional repressor Fep1. In contrast, when iron levels are low, the transcription ofyhb1+is derepressed and further induced in the presence of the NO donor DETANONOate. Cells lacking Yhb1 or expressing inactive forms of Yhb1 fail to grow in a hemin-dependent manner when exposed to DETANONOate. Similarly, loss of function of the heme transporter Str3 phenocopies the effects of Yhb1 disruption by causing hypersensitivity to DETANONOate under hemin-dependent culture conditions. Coimmunoprecipitation and bimolecular fluorescence complementation assays demonstrate the interaction between Yhb1 and the heme transporter Str3. Collectively, our findings unveil a novel pathway for activating Yhb1, fortifying yeast cells against nitrosative stress.
Engineering customized viral receptors for various coronaviruses
Authors: Liu Peng , Huang Meiling , Guo Hua , Si Junyu , Chen Yuanmei , Wang Chunli , Yu Xiao , Shi Lulu , Xiong Qing , Ma Chenbao , Tong Fei , Liu Chen , Chen Jing , Guo Ming , Li Jing , Shi Zheng-Li , Yan Huan
Published: March 2024

Coronaviruses display versatile receptor usage, yet in-depth characterization of coronaviruses lacking known receptor identities has been impeded by the absence of feasible infection models. Here, we developed an innovative strategy to engineer functional customized viral receptors (CVRs). The modular design relies on building receptor frameworks comprising various function modules and generating specific epitope-targeting viral binding domains. We showed the key factors for CVRs to efficiently facilitate spike cleavage, membrane fusion, pseudovirus entry, and authentic virus amplification for various coronaviruses, resembling their native receptors. Applying this strategy, we delineated the accessible receptor binding epitopes for functional SARS-CoV-2 CVR design and elucidated the mechanism of entry supported by an amino-terminus domain (NTD) targeting S2L20-CVR. Furthermore, we created CVR-expressing cells for assessing antibodies and inhibitors against 12 representative coronaviruses from six subgenera, most of which lacking known receptors. Notably, a pan-sarbecovirus CVR supported entry of various sarbecoviruses, as well as amplification of a replicable HKU3 pseudovirus and the authentic strain RsHuB2019A. Through combining an HKU5-specific CVR with reverse genetics, we successfully rescued and cultured wild-type and fluorescence protein-incorporated HKU5, a receptor-unidentified merbecovirus. Our study demonstrated the great potential of CVR strategy in establishing native receptor-independent infection models, paving the way for studying various viruses that are challenging to culture due to the lack of susceptible cells.
Detection of pathogens and antimicrobial resistant genes from urine within 5 hours using Nanopore sequencing
Authors: Bellankimath Anurag Basavaraj , Chapagain Crystal , Branders Sverre , Ali Jawad , Wilson Robert C , Bjerklund Johansen Truls E. , Ahmad Rafi
Published: March 2024

Purpose

Urinary Tract Infection (UTI) is a prevalent global health concern accounting for 1-3% of primary healthcare visits. The current methods for UTI diagnosis have a high turnaround time of 3-5 days for pathogen identification and susceptibility testing. This work is a proof-of-concept study aimed at determining the detection limit by establishing a culture and amplification-free DNA extraction methodology from spiked urine samples followed by real-time Nanopore sequencing and data analysis.

Methods

This study first establishes an optical density culture-based method for spiking healthy urine samples with the six most prevalent uropathogens. Pathogens were spiked at two clinically significant concentrations of 103and 105CFU/ml. Three commercial DNA extraction kits were investigated based on the quantity of isolated DNA, average processing time, elution volume and the average cost incurred per extraction. The outperforming kit was used for direct DNA extraction and subsequent sequencing on MinION and Flongle flowcells.

Results

The Blood and Tissue kit outperformed the other kits. All pathogens were identified at a concentration of 105CFU/ml within ten minutes, and the corresponding AMR genes were detected within three hours of the sequencing start. The overall turnaround time including the DNA extraction and sequencing steps was five hours. Moreover, we also demonstrate that the identification of some pathogens and antibiotic-resistance genes was possible at a spike concentration of 103CFU/mL.

Conclusion

This study shows great promise toward reducing the time required for making an informed antibiotic administration from approximately 48 hours to five hours thereby reducing the number of empirical doses and saving lives.
Regulation of Arabidopsis polyamine acetylation by NATA1 and NATA2
Authors: Hameed Umar F. Shahul , Lou Yann-Ru , Yan Jian , Guzman Vega Francisco Javier , Aleksenko Ekaterina , Briozzo Pierre , Morera Solange , Jander Georg , Arold Stefan T.
Published: March 2024

Polyamines have vital functions in organisms, including bacteria, plants, and animals, with key roles in growth, development, and stress responses. Spermine/spermidineN1-acetyl transferases (SSATs) regulate polyamine abundance by catalysing theirN-acetylation, thereby reducing the pool of polyamines and producing other bioactive components. The regulatory mechanisms controlling SSAT enzymes are incompletely understood. Here, we investigate the biological role and regulation of the two SSAT isoforms present inArabidopsis thaliana,N-ACETYLTRANSFERASE ACTIVITY (NATA) 1 and 2. We show that NATA2 is a heat-stable isoform, induced in response to heat. Intriguingly, anata2knockout mutation proved beneficial for growth and pathogen defence under heat stress in Arabidopsis, aligning with the stress-mitigating effect of polyamines. In contrast, the double knockout ofnata1andnata2was lethal, highlighting the essential role of basal SSAT activity. Our numerous crystal structures of both NATAs, supported by functional assays, revealed that stress-produced acidic metabolites can selectively inhibit polyamine acetylation by occupying the NATA substrate-binding pocket. This environment-responsive regulation mechanism may allow Arabidopsis to adjust the deleterious action of NATAs under stress conditions, without eliminating the enzyme. More generally, metabolite-ensemble inhibition may be a novel paradigm for non-genetic feedback regulation of plant enzymes.
Involvement of ArlI, ArlJ, and CirA in Archaeal Type-IV Pilin-Mediated Motility Regulation
Authors: Chatterjee Priyanka , Garcia Marco A. , Cote Jacob A. , Yun Kun , Legerme Georgio P. , Habib Rumi , Tripepi Manuela , Young Criston , Kulp Daniel , Dyall-Smith Mike , Pohlschroder Mecky
Published: March 2024

Many prokaryotes use swimming motility to move toward favorable conditions and escape adverse surroundings. Regulatory mechanisms governing bacterial flagella-driven motility are well-established, however, little is yet known about the regulation underlying swimming motility propelled by the archaeal cell surface structure, the archaella. Previous research showed that deletion of the adhesion pilins (PilA1-6), subunits of the type IV pili cell surface structure, renders the model archaeonHaloferax volcaniinon-motile. In this study, we used EMS mutagenesis and a motility assay to identify motile suppressors of the ΔpilA[1-6] strain. Of the eight suppressors identified, six contain missense mutations in archaella biosynthesis genes,arlIandarlJ. Overexpression of thesearlIandarlJmutant constructs in the respective multi-deletion strains ΔpilA[1-6]ΔarlIand ΔpilA[1-6]ΔarlJconfirmed their role in suppressing the ΔpilA[1-6] motility defect. Additionally, three suppressors harbor co-occurring disruptive missense and nonsense mutations incirA, a gene encoding a proposed regulatory protein. A deletion ofcirAresulted in hypermotility, whilecirAoverexpression in wild-type cells led to decreased motility. Moreover, qRT-PCR analysis revealed that in wild-type cells, higher expression levels ofarlI,arlJ, and the archaellin genearlA1were observed in motile early-log phase rod-shaped cells compared to non-motile mid-log phase disk-shaped cells. Conversely, ΔcirAcells, which form rods during both early and mid-log phases, exhibited similar expression levels ofarlgenes in both growth phases. Our findings contribute to a deeper understanding of the mechanisms governing archaeal motility, highlighting the involvement of ArlI, ArlJ, and CirA in pilin- mediated motility regulation.

Importance

Archaea are close relatives of eukaryotes and play crucial ecological roles. Certain behaviors, such as swimming motility, are thought to be important for archaeal environmental adaptation. Archaella, the archaeal motility appendages, are evolutionarily distinct from bacterial flagella, and the regulatory mechanisms driving archaeal motility are largely unknown. Previous research has linked the loss of type IV pili subunits to archaeal motility suppression. This study reveals threeHaloferax volcaniiproteins involved in pilin-mediated motility regulation, offering a deeper understanding of motility regulation in this understudied domain while also paving the way for uncovering novel mechanisms that govern archaeal motility. Understanding archaeal cellular processes will help elucidate the ecological roles of archaea as well as the evolution of these processes across domains.
Identification of new resistance QTL regions in loquat cultivar ‘Champagne’ againstPseudomonas syringaepv.eriobotryaegroup C
Authors: Koga Shogo , Kawaguchi Ryusei , Tanaka Tsunami , Moriya Shigeki , Hiehata Naofumi , Kabashima Koji , Nagano Atushi J. , Nagano Yukio , Fukuda Shinji
Published: March 2024

Loquat canker, caused byPseudomonas syringaepv.eriobotryae, is a bacterial disease that infects loquat (Eriobotrya japonica) and has been reported in several countries. Three pathotypes, A, B, and C, have been reported in Japan. The loquat cultivar ‘Champagne’ is resistant to the loquat canker group C and possesses a qualitative trait governed by a recessive homozygouspse-cgene located on Linkage Group 3 (LG3), and quantitative traits located at unidentified loci. In this study, we identified novel quantitative trait loci (QTL) regions for resistance to group C in this cultivar. A seedling population with ‘Tanaka’ (Pse-c/Pse-c) crossed with ‘Champagne’ (pse-c/pse-c) was tested. The genetic map of ‘Champagne’ includes a total of 1,016 SNP markers mapped across 17 LGs, covering a total distance of 1,301 cM and an average marker density of 1.4 cM/locus. In addition to minor potential QTLs, the major QTL for resistance to loquat canker group C was detected in the upper region of LG14, with the QTL contributing 6.9% to the disease index. The results of this study open new possibilities for resistance breeding against this disease.

Highlights.

A total of 1,016 SNP markers were mapped on a linkage map consisting of 17 linkage groups with a total distance of 1,301 cM.

QTL analysis revealed a novel resistance QTL region in ‘Champagne’ against loquat canker group C in the upper part of the LG14.

The identified QTLs in this study provide new possibilities for resistance breeding in loquat.
Pure yeasts selected from fermenting pear juice from the Lower Austrian Mostviertel region and their suitability for pear wine production
Authors: Gangl H. , Tscheik G. , Tiefenbrunner W.
Published: March 2024

If spontaneous fermentation is not carried out, commercially available pure yeasts, which are actually intended for the production of wines from grapes, are often used for the production of pear wines. Pear juice is clearly different from grape juice, e.g. due to the significantly greater difference in the ratio of fructose to glucose or the absence of tartaric acid. For this reason, the commercially available pure yeasts may be suboptimal for pear wine production. They were therefore compared with yeasts isolated from pear juice that had been purely cultivated with regard to their suitability for pear wine production.

Overall, the yeasts isolated from fermenting pear juice proved to be more suitable for pear wine production. This is not only the result of the tasting of the wines fermented in 25-litre glass flasks, but also follows very clearly from the multivariate comparison both for the basic chemistry and for the spectrum of aroma components. Density and malic acid concentration were higher in wines produced with yeasts selected from fermenting pear juice. More substances from the "fruity" and especially "fruity-sweet" flavour groups were found in these wines in comparatively higher concentrations.

For pear wine production, it is therefore advisable to isolate suitable yeasts from pear juice for pure cultivation.
Antibacterial T6SS1 cluster identification and bioinformatics characterization of their putative effectors in Shiga toxin-producingEscherichia coli
Authors: Riviere Nahuel A. , Casabonne María Carolina , Smith Libia Y. , Marques da Silva Wanderson , Cataldi Ángel A. , Larzábal Mariano
Published: March 2024

Shiga toxing-producingEscherichia coli(STEC) O22:H8 strain is a serotype occasionally isolated in Argentinian cattle. Preliminary works showed that the cattle carrying STEC O22:H8 strains could not be experimentally colonized by EHEC O157:H7 strain. The type 6 secretion system (T6SS) is one of the most versatile virulence mechanisms involved in delivering effectors, particularly the T6SS1 translocate antibacterial toxins effectors during bacterial competition for niche-space. In this work, we could evidence the molecular bases of the success of STEC O22:H8 (154) strain during bacterial competition against EHEC O157:H7 strains. The genome sequence of STEC O22:H8 (154) allowed us to identify a complete T6SS1 cluster. In addition, we identify and characterized several putative T6SS1-antibacterial effectors encoded inside the T6SS1 clusters and in genomic pathogenic islands. Competition assays against EHEC O157:H7 strain confirmed the antibacterial activity of STEC O22:H8 (154) strainin vitro. Considering the absent of T6SS1 in STEC strains, we proposed the recent horizontal transfer acquisition and the most probably donor belong to the sameEscherichia colispecies. A safe STEC O22:H8 (154)Δstxwould be used as a new strategy to fight STECs in bovine intestinal colonization, leading in a reduction in beef contamination and consequently HUS cases in humans.
Microbunch rotation in an x-ray free-electron laser using a first-order achromatic bend
Authors: Margraf Rachel A. , MacArthur James P. , Marcus Gabriel , Nuhn Heinz-Dieter , Lutman Alberto , Halavanau Aliaksei , Zhang Zhen , Huang Zhirong
Published: March 2024

Electrons in an x-ray free electron laser (XFEL) develop periodic density fluctuations, known as microbunches, which enable the exponential gain of x-ray power in an XFEL. When an electron beam microbunched at a hard x-ray wavelength is kicked, microbunches are often washed out due to the dispersion and R56 of the bend. An achromatic (dispersion-free) bend with a small R56, however, can preserve microbunches, which rotate to follow the new trajectory of the electron bunch. Rotated microbunches can subsequently interact in a repointed undulator to produce a new beam of off-axis x rays. In this work, we demonstrate hard x-ray multiplexing in the Linac Coherent Light Source hard x-ray undulator line using microbunch rotation through a 10  μrad first-order-achromatic bend created by transversely offsetting quadrupole magnets in the FODO lattice. Quadrupole offsets are determined analytically from beam-matrix theory. We also discuss the application of microbunch rotation to out-coupling a cavity-based XFEL.

Published by the American Physical Society
2024
Berry curvature inside a
PT
-symmetry protected exceptional surface
Authors: Wang P. , Jin L. , Song Z.
Published: March 2024

A three-dimensional non-Hermitian Hamiltonian with parity-time symmetry can exhibit a closed exceptional surface (EP surface) in momentum space, which is a non-Hermitian deformation of the degeneracy line. Since the degeneracy line lacks an internal space, the distributions of Berry curvature inside the EP surface become particularly intriguing. This paper studies the distributions taking a toruslike EP surface as an example. In a meridian cross section, the Berry connection exhibits a vortexlike field with only angular components, while the Berry curvature is perpendicular to this cross section; in a equatorial cross section, the Berry curvature forms a closed curve surrounding the central genus. Both Berry connection and curvature converge along the coplanar axis and diverge at the surface. We find the Berry flux depends on the radius of the integration region and is not quantized inside the EP torus. Approaching the surface, the Berry flux tends to infinity and the dynamical phase oscillates violently. We point out that the streamlines of Berry curvature can be used to estimate the zero or nonzero Berry flux. We generalize the above patterns to the case of EP surfaces with complex shapes and present a proposal of realizing the EP surface in an electrical circuit. Our research outcomes enhance the comprehension of EP surfaces and the topological characteristics of non-Hermitian systems with parity-time (PT) symmetry.

Published by the American Physical Society
2024
Hadron-quark transition and chiral symmetry restoration at high density
Authors: Kouno Hiroaki , Kashiwa Kouji
Published: March 2024

A simple phenomenological hybrid hadron-quark model with excluded volume effects of baryons and chiral dynamics is investigated. The hybrid equation of state naturally connects the low-density baryonic matter with the high-density quark matter. In the intermediate region, a phase, which cannot be regarded as pure hadron matter or pure quark matter, appears. In this model, there is a possibility that the abrupt first-order-like transition to pure quark matter induces the strong chiral symmetry restoration and the speed of sound has a large peak at considerable large density.

Published by the American Physical Society
2024
Windows of opportunity, strategic cognition and enterprise digital transformation
Authors: Zang Shuwei , Sun Mengyuan , Wang Qimeng , Wang Haofu , Tian Shanwu
Published: March 2024

Purpose

The purpose of this paper is to discuss how enterprises can effectively perceive and use the digital opportunities brought about by digital technologies and dynamic environments and how they can enhance their capabilities to realize digital transformation and adapt to the development of the digital economy era.

Design/methodology/approach

Based on the windows of opportunity theory and strategic cognition theory, this paper conducts an empirical analysis of the questionnaire data of 268 enterprises and discusses the influence of external windows of opportunity and internal windows of opportunity on the digital transformation of enterprises, as well as the action mechanism of strategic cognition and entrepreneurship.

Findings

The results show that both the external windows of opportunity and the internal windows of opportunity have significant positive effects on the digital transformation of enterprises. Strategic cognition plays a partial mediating role in the external windows of opportunity and the internal windows of opportunity influencing the enterprise digital transformation process. Entrepreneurship plays a positive regulatory role in the process of external windows of opportunity and internal windows of opportunity influencing strategic cognition.

Originality/value

This paper deepens the relationship between internal and external windows of opportunity and enterprise digital transformation and contributes a new theoretical cognition. This paper integrates the strategic cognition theory to clarify the complex process mechanism of digital transformation using external situational opportunities and internal capabilities. This paper introduces entrepreneurship into the path mechanism of digital transformation and expands the characteristics of the study of digital transformation antecedents to the individual level within the enterprise.
Wind turbine emulator using three-phase IM controlled through an adaptive reactive power estimator fed by soft-VSI topology
Authors: Zerzeri Mouna , Moussa Intissar , Khedher Adel
Published: March 2024

Purpose

The purpose of this paper aims to design a robust wind turbine emulator (WTE) based on a three-phase induction motor (3PIM).

Design/methodology/approach

The 3PIM is driven by a soft voltage source inverter (VSI) controlled by a specific space vector modulation. By adjusting the appropriate vector sequence selection, the desired VSI output voltage allows a real wind turbine speed emulation in the laboratory, taking into account the wind profile, static and dynamic behaviors and parametric variations for theoretical and then experimental analysis. A Mexican hat profile and a sinusoidal profile are therefore used as the wind speed system input to highlight the electrical, mechanical and electromagnetic system response.

Findings

The simulation results, based on relative error data, show that the proposed reactive power control method effectively estimates the flux and the rotor time constant, thus ensuring an accurate trajectory tracking of the wind speed for the wind emulation application.

Originality/value

The proposed architecture achieves its results through the use of mathematical theory and WTE topology combine with an online adaptive estimator and Lyapunov stability adaptation control methods. These approaches are particularly relevant for low-cost or low-power alternative current (AC) motor drives in the field of renewable energy emulation. It has the advantage of eliminating the need for expensive and unreliable position transducers, thereby increasing the emulator drive life. A comparative analysis was also carried out to highlight the online adaptive estimator fast response time and accuracy.
The Olympus scandal – the dark side of social networks and corporate culture
Authors: Ilieva Maria
Published: March 2024

Purpose

This study aims to build on the well-documented case of the Olympus scandal to dissect how social networks and corporate culture enabled corporate elites to commit fraud across multiple generations of leaders.

Design/methodology/approach

A flexible pattern matching approach was used to identify matches and mismatches between behavioural theory in corporate governance and the patterns observed in data from diverse sources.

Findings

The study applies the behavioural theory of corporate governance from different perspectives. Social networks and relationships were essential for the execution of the fraud and keeping it secret. The group of corporate elites actively created opportunities for committing misappropriation. This research presents individuals committing embezzlement because the opportunity already exists, and they can enrich themselves. The group of insiders who committed the fraud elaborated the rationalizations to others and asked outside associates to help rationalise the activities, while usually individuals provide rationalizations to themselves only.

Practical implications

The social processes among actors described in this case can inform the design of mechanisms to detect these behaviours in similar contexts.

Originality/value

This study provides both perspectives on the fraud scandal: the one of the whistle-blowers, and the opposing side of the transgressors and their associates. The extant case studies on Olympus presented the timeframe of the scandal right after the exposure. The current study dissects the events during the fraud execution and presents the case in a neutral or a negative light.