bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep CANALs: a deep learning approach to refining the canalization theory of psychopathology
Authors: Juliani Arthur , Safron Adam , Kanai Ryota
Published: March 2024

Psychedelic therapy has seen a resurgence of interest in the last decade, with promising clinical outcomes for the treatment of a variety of psychopathologies. In response to this success, several theoretical models have been proposed to account for the positive therapeutic effects of psychedelics. One of the more prominent models is “RElaxed Beliefs Under pSychedelics,” which proposes that psychedelics act therapeutically by relaxing the strength of maladaptive high-level beliefs encoded in the brain. The more recent “CANAL” model of psychopathology builds on the explanatory framework of RElaxed Beliefs Under pSychedelics by proposing that canalization (the development of overly rigid belief landscapes) may be a primary factor in psychopathology. Here, we make use of learning theory in deep neural networks to develop a series of refinements to the original CANAL model. Our primary theoretical contribution is to disambiguate two separate optimization landscapes underlying belief representation in the brain and describe the unique pathologies which can arise from the canalization of each. Along each dimension, we identify pathologies of either too much or too little canalization, implying that the construct of canalization does not have a simple linear correlation with the presentation of psychopathology. In this expanded paradigm, we demonstrate the ability to make novel predictions regarding what aspects of psychopathology may be amenable to psychedelic therapy, as well as what forms of psychedelic therapy may ultimately be most beneficial for a given individual.
Effects of Exogenous Application of Methyl Jasmonate and Salicylic Acid on the Physiological and Molecular Response of ‘Dusa’ Avocado to Rosellinia necatrix
Authors: Moreno-Pérez Ana , Martínez-Ferri Elsa , van den Berg Noëlani , Pliego Clara
Published: March 2024

Methyl jasmonate (MeJA) and salicylic acid (SA) are important in mediating plant responses to abiotic and biotic stresses. MeJA and SA can act as elicitors by triggering plant defense responses similar to those induced by pathogens and may even provide long-term protection against them. Thus, exogenous application of MeJA and SA could protect susceptible avocado plants against white root rot (WRR) disease caused by the necrotrophic fungus Rosellinia necatrix, one of the main diseases affecting avocado orchards. This work evaluates the effects of MeJA or SA on the physiological and molecular response of susceptible ‘Dusa’ avocado rootstock and their ability to provide some protection against WRR. The application of MeJA and SA in avocado increased photoprotective mechanisms (nonphotochemical chlorophyll fluorescence quenching) and upregulated the glutathione S-transferase, suggesting the triggering of mechanisms closely related to oxidative stress relief and reactive oxygen species scavenging. In contrast to SA, MeJA’s effects were more pronounced at the morphoanatomical level, including functional traits such as high leaf mass area, high stomatal density, and high root/shoot ratio, closely related to strategies to cope with water scarcity and WRR disease. Moreover, MeJA upregulated a greater number of defense-related genes than SA, including a glu protease inhibitor, a key gene in avocado defense against R. necatrix. The overall effects of MeJA increased ‘Dusa’ avocado tolerance to R. necatrix by inducing a primed state that delayed WRR disease symptoms. These findings point toward the use of MeJA application as an environmentally friendly strategy to mitigate the impact of this disease on susceptible avocado orchards.
The human MIF polymorphism CATT7 enhances pro‐inflammatory macrophage polarization in a clinically relevant model of allergic airway inflammation
Authors: Dunbar Hazel , Hawthorne Ian J. , McNamee Eóin N. , Armstrong Michelle E. , Donnelly Seamas C. , English Karen
Published: March 2024

High level expression of the pro‐inflammatory cytokine macrophage migration inhibitory factor (MIF) has been associated with severe asthma. The role of MIF and its functional promotor polymorphism in innate immune training is currently unknown. Using novel humanized CATT7 MIF mice, this study is the first to investigate the effect of MIF on bone marrow‐derived macrophage (BMDM) memory after house dust mite (HDM) challenge. CATT7 BMDMs demonstrated a significant primed increase in M1 markers following HDM and LPS stimulation, compared to naive mice. This M1 signature was found to be MIF‐dependent, as administration of a small molecule MIF inhibitor, SCD‐19, blocked the induction of this pro‐inflammatory M1‐like phenotype in BMDMs from CATT7 mice challenged with HDM. Training naive BMDMs in vitro with HDM for 24 h followed by a rest period and subsequent stimulation with LPS led to significantly increased production of the pro‐inflammatory cytokine TNFα in BMDMs from CATT7 mice but not WT mice. Addition of the pan methyltransferase inhibitor MTA before HDM training significantly abrogated this effect in BMDMs from CATT7 mice, suggesting that HDM‐induced training is associated with epigenetic remodelling. These findings suggest that trained immunity induced by HDM is under genetic control, playing an important role in asthma patients with the high MIF genotypes (CATT6/7/8).
The DNP project
Authors: Melander Sheila , Hampton Debra , Makowski Andrew , Falls Candice , Tovar Elizabeth
Published: March 2024

Twenty years ago, pioneer Doctor of Nursing Practice (DNP) program students completed the first DNP projects. Today, DNP projects remain a requirement for graduation. This article illustrates how the DNP project can be integrated throughout the DNP curriculum to maximize effectiveness and promote the introduction, reinforcement, and evaluation of competencies in the new American Association of Colleges of Nursing Essentials.
Predictive Value of Carotid-femoral Pulse Wave Velocity for Major Adverse Cardiovascular Events and All-cause Mortality in Different Age Groups of a Chinese Community
Authors: Zheng Jin , Wang Xiaona , Mao Li , Ye Ping
Published: March 2024

Objective:

To investigate the predictive value of carotid-femoral pulse wave velocity (cf-PWV) for assessing major adverse cardiovascular events (MACE) and all-cause mortality in different age groups of a Chinese community.

Methods:

This is an observational study which enrolled 1,325 individuals from a community in Beijing from September 2007 to October 2018. They were classified based on age into <65-year-old (n = 572) and ≥65-year-old (n = 753) groups, and on cf-PWV into cf-PWV <12 m/s (n = 501) and cf-PWV≥12 m/s (n = 824) group. The incidence rates of MACE and all-cause mortality were recorded for both the groups during the follow-up period of 9.5 years. The predictive value of cf-PWV for MACE and all-cause mortality in the 2 age groups was estimated using the Cox proportional hazards regression models.

Results:

The baseline cf-PWV showed positive correlation with age (r = 0.462, P < 0.001). During the follow-up period, 191 MACE and 84 all-cause mortality cases were recorded in the study population. The incidence rates of MACE (χ
2 = 27.196, P < 0.001) and all-cause mortality (χ
2 = 9.473, P = 0.002) were significantly higher in subjects with cf-PWV ≥12 m/s than in subjects with cf-PWV <12 m/s. Cox proportional hazards regression model analyses demonstrated that cf-PWV was an independent risk factor in the <65-year-old group for MACE (hazard ratio: 1.310; 95% confidence interval: 1.007–1.560; P = 0.038) and all-cause mortality (hazard ratio: 1.412; 95% confidence interval: 1.133–1.936; P = 0.005) after adjusting for several risk factors. However, both univariate and multivariate analyses demonstrated that cf-PWV was not an independent risk factor for MACE or all-cause mortality in the ≥65-year-old group (P > 0.05).

Conclusion:

cf-PWV, a measure of arterial stiffness, emerged as an independent risk factor for MACE and all-cause mortality in subjects below 65 years of age.
Artificial Intelligence and the National Violent Death Reporting System
Authors: Lindley Lisa C. , Policastro Christina N. , Dosch Brianne , Ortiz Baco Joshua G. , Cao Charles Q.
Published: March 2024

As the awareness on violent deaths from guns, drugs, and suicides emerges as a public health crisis in the United States, attempts to prevent injury and mortality through nursing research are critical. The National Violent Death Reporting System provides public health surveillance of US violent deaths; however, understanding the National Violent Death Reporting System's research utility is limited. The purpose of our rapid review of the 2019-2023 literature was to understand to what extent artificial intelligence methods are being used with the National Violent Death Reporting System. We identified 16 National Violent Death Reporting System artificial intelligence studies, with more than half published after 2020. The text-rich content of National Violent Death Reporting System enabled researchers to center their artificial intelligence approaches mostly on natural language processing (50%) or natural language processing and machine learning (37%). Significant heterogeneity in approaches, techniques, and processes was noted across the studies, with critical methods information often lacking. The aims and focus of National Violent Death Reporting System studies were homogeneous and mostly examined suicide among nurses and older adults. Our findings suggested that artificial intelligence is a promising approach to the National Violent Death Reporting System data with significant untapped potential in its use. Artificial intelligence may prove to be a powerful tool enabling nursing scholars and practitioners to reduce the number of preventable, violent deaths.
Cutaneous Angiosarcoma Subtypes: A Quantitative Systematic Review of Demographics, Treatments, and Outcomes Within Published Patient-Level Cases
Authors: Kwapnoski Zachary , Clarey Dillon , Ma Jihyun , Schmidt Cynthia M. , Wysong Ashley
Published: March 2024

BACKGROUND

Cutaneous angiosarcoma (cAS) is a highly aggressive malignancy arising from the vascular endothelium. Given its rarity, there is insufficient data detailing patient demographics, management, and survival outcomes.

OBJECTIVE

To systematically compile published patient-level cases of cAS and to quantify and analyze data on demographics, management, and outcomes while determining prognostic indicators.

MATERIALS AND METHODS

Searches of EBSCOhost, MEDLINE, EMBASE, and the Cochrane Library generated 1,500 cases of cAS with individual level data available. PRISMA guidelines were followed.

RESULTS

Cutaneous angiosarcoma presented most often on the scalp of elderly men. Metastasis occurred in 36.3% of cases. Aggregate 5-year survival was 31.6% with the median survival of 25 months. The best 5-year survival was in the radiation-associated subtype (48.8%), whereas the worst was in the Stewart–Treves subtype (21.6%). Using multivariate analysis, gender, age group, disease subtype, treatment modality, and metastasis at presentation had significant effects on survival outcomes (p < .05).

CONCLUSION

The breadth of information obtained enables this study to serve as a resource that clinicians may reference when they encounter cAS.
Rapid intervention team strategy improves intervention quality for patients undergoing hemodialysis with arteriovenous shunt dysfunction or failure
Authors: Wang Szu-Han , Ko Chih-Chang , Kuo Yi-Ling , Chiu Yu-Wen , Wen Jih-Sheng , Wang Ming-Cheng , Chao Ting-Hsing , Chang Hsien-Yuan
Published: March 2024

Background:

Vascular access dysfunction is a great burden for hemodialysis patients. Early intervention of a dysfunctional arteriovenous shunt is associated with higher technical success and may improve midterm patency. This trial aimed to estimate the feasibility of a new system, the “rapid intervention team” (RIT) strategy.

Methods:

We recruited hemodialysis patients who visited our hospital because of arteriovenous shunt dysfunction or failure to undergo an RIT strategy from September 1, 2019 to December 31, 2022. In addition, we included a control group comprising patients who underwent percutaneous intervention for arteriovenous shunt dysfunction or failure before this strategy was implemented from February 1, 2017 to December 31, 2022. Case number, time to intervention, all-cause mortality, cumulative survival rate, and number of patients who required temporary dialysis catheter insertion and recreation were compared between the two groups. The primary endpoints were double-lumen insertion, a composite outcome involving permanent catheter insertion, and the need for recreation. The secondary endpoint was all-cause mortality.

Results:

We enrolled 1054 patients, including 544 (51.6%) and 510 (48.4%) in the RIT and control groups, respectively. Even with the coronavirus disease of 2019 (COVID-19) pandemic, the number of cases significantly increased after the implementation of the RIT strategy (from 216 in 2019 to 828 in 2022, p for trend <0.001). The RIT group had a shortened time to intervention (p for trend <0.001). The implementation of the RIT strategy was significantly associated with a reduced risk of insertion of a temporary double-lumen catheter and recreation of vascular access (1% vs 6% and 1% vs 28%, respectively; both p < 0.01). The cumulative survival rate was not significantly different between the RIT and control groups (p = 0.16).

Conclusion:

The implementation of the RIT strategy improves the quantity and quality of percutaneous transluminal intervention for arteriovenous shunt dysfunction or failure in patients undergoing hemodialysis.
Connor-Davidson Resilience Scale: a systematic review psychometrics properties using the COSMIN
Authors: Sharif-Nia Hamid , Sánchez-Teruel David , Sivarajan Froelicher Erika , Hejazi Sima , Hosseini Lida , Khoshnavay Fomani Fatemeh , Moshtagh Mozhgan , Mollaei Fereshteh , Goudarzian Amir Hossein , Babaei Amir
Published: March 2024

Background:

Psychometrical evaluation of persons of diverse contexts and different populations, including general or clinical.

Objective:

This review study aimed to evaluate the psychometrics quality of resilience scales.

Methods:

International and Iranian databases were searched with MESH terms, including “psychometric”, “validity”, “reliability”, “Connor-Davidson resilience scale”, “Resilience scale”, for published articles up to 1 February 2023. For each of the selected studies, the risk of bias was evaluated using the COSMIN Risk of Bias Checklist. Then the COSMIN checklist was used to evaluate the entire text of the article for methodological quality.

Results:

Considering the inclusion criteria, 80 documents were evaluated. According to the COSMIN’s criteria for evaluating the risk of bias, the current study findings revealed the included studies’ limitations in assessing the three versions of CD-RISC cross-cultural and content validity as well as their stability (e.g. conducting test re-test), whereas the majority of psychometric studies of CD-RISC-25, and CD-RISC-2 rated as very good or adequate in terms of structural validity. In terms of quality assessment of the included studies, the current study indicated that investigating the structural validity of the CD-RISC was mainly done based on exploratory factor analysis (EFA), and confirmatory factor analysis was absent.

Conclusion:

The general result indicates the acceptability of the quality of the studies. However, concerns for measurement properties such as responsiveness and criterion validity as well as the standard error of measurement have been neglected.
Nutrition Management of the Adult Patient With Necrotizing Fasciitis
Authors: Zahid Saba , Parker Anna
Published: March 2024

Necrotizing fasciitis is an invasive, life-threatening infection of the tissues. Necrotizing fasciitis is not a commonly seen infection, making it a challenging infection for many clinicians to treat and manage due to a lack of familiarity with the disease process. Further, there is limited research and guidance available regarding nutrition care for patients recovering from necrotizing fasciitis. This article presents a case study and highlights how currently available guidelines can be critically applied by dietitians to provide appropriate nutrition care in a relatively unfamiliar patient population.
The Effect of β-Hydroxy-β-Methylbutyrate on Muscle Strength and Functional Outcomes in Older Adults
Authors: Mendes Joana , Guerra Rita S. , Sousa Ana S.
Published: March 2024

Nutritional intervention is increasingly being recognized as playing an important role in functional status. The supplementation with β‑hydroxy-β-methylbutyrate (HMB), which is a metabolite of an essential amino acid, may be an effective nutritional intervention to improve muscle strength and functionality in older adults. The aim of this narrative review was to present an updated overview of the effects of HMB supplementation in older adults, specifically on muscle strength and functional outcomes. A PubMed database search was performed and only randomized controlled trial studies were included. More than half of the 14 analyzed studies reported that HMB supplementation improved muscle strength and other functional outcomes. HMB supplementation has demonstrated some promising effects on muscle strength and functional outcomes in older adults with different conditions of health and physical activity.
Creation, Validation, and Use of Photo-Based Smartphone Application for Dietary Fiber Counting Among University Students
Authors: Sharif Israa , Badrasawi Manal , Zidan Souzan , Zghier Hana , Abu Sunaina Raghad , Abu Mazer Tamara
Published: March 2024

The main aim of this study was to develop a smartphone application specializing in assessing dietary fiber intake of university students. The validity of the application was tested among 45 volunteers, their daily intake was recorded for 3 days using the Daily Fiber application, and intakes were compared with a 3-day food record matched to the same days. The mean intake of dietary fiber using the 3-day food record and our application was 10.08 ± 4.48 and 10.21 ± 4.64 g/d, respectively (P < .01). Overall, Daily Fiber is a promising tool for assessing dietary fiber intake among undergraduates.
Ruicaihuangia caeni gen. nov., sp. nov., a novel taxon within the family Microbacteriaceae isolated from sludge
Authors: Liu Le , Geng Keke , Lv Yu , Zhang Qi , Chen Gang , Cheng Dan , Shao Jiahui , He Jian , Shen Qirong
Published: March 2024

A Gram-stain-positive bacterium, designated YN-L-19T, was isolated from a sludge sample collected from a pesticide-manufacturing plant. Cells of YN-L-19T were strictly aerobic, non-spore-forming, non-motile and ovoid-shaped. Colonies were small, smooth and yellow. Growth occurred at 10–37 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, 7.0) and 0–3.0 % (w/v) NaCl (optimum 0.5 %). Phylogenetic analysis based on genome and 16S rRNA gene sequences indicated that YN-L-19T was affiliated to the family Microbacteriaceae and most closely related to Diaminobutyricimonas aenilata, Terrimesophilobacter mesophilus, Planctomonas deserti and Curtobacterium luteum. The major cellular fatty acids of YN-L-19T were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The predominant menaquinone was MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid and one unidentified lipid. The average amino acid identity values between strain YN-L-19T and the related strains were 57.9–61.9 %, which were below the genus boundary (70 %). On the basis of the evidence presented in this study, strain YN-L-19T represents a novel species of a new genus in the family Microbacteriaceae, for which the name Ruicaihuangia caeni gen. nov., sp. nov. (type strain YN-L-19T=CCTCC AB 2022401T= KCTC 49935T) is proposed.
Bosea beijingensis sp. nov., Telluria beijingensis sp. nov. and Agrococcus beijingensis sp. nov., isolated from baijiu mash
Authors: Gu Hao-Yue , Hao Shu-Yue , Sun Zhan-Bin , Xu Jia-Liang , Ren Qing , Pan Han-Xu
Published: March 2024

The baijiu fermentation environment hosts a variety of micro-organisms, some of which still remain uncultured and uncharacterized. In this study, the isolation, cultivation and characterization of three novel aerobic bacterial strains are described. The cells of strain REN20T were Gram-negative, strictly aerobic, motile and grew at 26–37 °C, at pH 6.0–9.0 and in the presence of 0–5.0   % (w/v) NaCl. The cells of strain REN29T were Gram-negative, strictly aerobic, motile and grew at 15–30 °C, at pH 6.0–9.0 and in the presence of 0–10.0   % (w/v) NaCl. The cells of strain REN33T were Gram-positive, strictly aerobic, motile and grew at 15–37 °C, at pH 5.0–10.0 and in the presence of 0–7.0   % (w/v) NaCl. The digital DNA–DNA hybridization and average nucleotide identity by orthology values between type strains in related genera and REN20T (20.3–36.8 % and 79.8–89.9  %), REN29T (20.3–36.8  % and 74.5–88.5  %) and REN33T (22.6–48.6  % and 75.8–84.2  %) were below the standard cut-off criteria for the delineation of bacterial species, respectively. Based on polyphasic taxonomy analysis, we propose three new species, Bosea beijingensis sp. nov. (=REN20T=GDMCC 1.2894T=JCM 35118T), Telluria beijingensis sp. nov. (=REN29T=GDMCC 1.2896T=JCM 35119T) and Agrococcus beijingensis sp. nov. (=REN33T=GDMCC 1.2898T=JCM 35164T), which were recovered during cultivation and isolation from baijiu mash.
Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism
Authors: Crowley Claire , Selvaraj Ajith , Hariharan Arvind , Healy Claire M. , Moran Gary P.
Published: March 2024

Fusobacterium nucleatum is an anaerobic commensal of the oral cavity associated with periodontitis and extra-oral diseases, including colorectal cancer. Previous studies have shown an increased relative abundance of this bacterium associated with oral dysplasia or within oral tumours. Using direct culture, we found that 75 % of Fusobacterium species isolated from malignant or potentially malignant oral mucosa were F. nucleatum subsp. polymorphum. Whole genome sequencing and pangenome analysis with Panaroo was carried out on 76 F. nucleatum subsp. polymorphum genomes. F. nucleatum subsp. polymorphum was shown to possesses a relatively small core genome of 1604 genes in a pangenome of 7363 genes. Phylogenetic analysis based on the core genome shows the isolates can be separated into three main clades with no obvious genotypic associations with disease. Isolates recovered from healthy and diseased sites in the same patient are generally highly related. A large repertoire of adhesins belonging to the type V secretion system (TVSS) could be identified with major variation in repertoire and copy number between strains. Analysis of intergenic recombination using fastGEAR showed that adhesin complement is shaped by horizontal gene transfer and recombination. Recombination events at TVSS adhesin genes were not only common between lineages of subspecies polymorphum, but also between different subspecies of F. nucleatum. Strains of subspecies polymorphum with low copy numbers of TVSS adhesin encoding genes tended to have the weakest adhesion to oral keratinocytes. This study highlights the genetic heterogeneity of F. nucleatum subsp. polymorphum and provides a new framework for defining virulence in this organism.
Optimising machine learning prediction of minimum inhibitory concentrations in Klebsiella pneumoniae
Authors: Batisti Biffignandi Gherard , Chindelevitch Leonid , Corbella Marta , Feil Edward J. , Sassera Davide , Lees John A.
Published: March 2024

Minimum Inhibitory Concentrations (MICs) are the gold standard for quantitatively measuring antibiotic resistance. However, lab-based MIC determination can be time-consuming and suffers from low reproducibility, and interpretation as sensitive or resistant relies on guidelines which change over time. Genome sequencing and machine learning promise to allow in silico MIC prediction as an alternative approach which overcomes some of these difficulties, albeit the interpretation of MIC is still needed. Nevertheless, precisely how we should handle MIC data when dealing with predictive models remains unclear, since they are measured semi-quantitatively, with varying resolution, and are typically also left- and right-censored within varying ranges. We therefore investigated genome-based prediction of MICs in the pathogen Klebsiella pneumoniae using 4367 genomes with both simulated semi-quantitative traits and real MICs. As we were focused on clinical interpretation, we used interpretable rather than black-box machine learning models, namely, Elastic Net, Random Forests, and linear mixed models. Simulated traits were generated accounting for oligogenic, polygenic, and homoplastic genetic effects with different levels of heritability. Then we assessed how model prediction accuracy was affected when MICs were framed as regression and classification. Our results showed that treating the MICs differently depending on the number of concentration levels of antibiotic available was the most promising learning strategy. Specifically, to optimise both prediction accuracy and inference of the correct causal variants, we recommend considering the MICs as continuous and framing the learning problem as a regression when the number of observed antibiotic concentration levels is large, whereas with a smaller number of concentration levels they should be treated as a categorical variable and the learning problem should be framed as a classification. Our findings also underline how predictive models can be improved when prior biological knowledge is taken into account, due to the varying genetic architecture of each antibiotic resistance trait. Finally, we emphasise that incrementing the population database is pivotal for the future clinical implementation of these models to support routine machine-learning based diagnostics.
A comparative study of plant phenotyping workflows based on three-dimensional reconstruction from multi-view images
Authors: Daiki Someno , Noshita Koji
Published: March 2024

With the world facing escalating food demand, limited agricultural land, and rapid environmental change, there is a growing need for data-driven sustainable agricultural management approaches. The proliferation of next-generation sequencers and sensor networks has reduced the cost of acquiring genomic and environmental data, respectively. However, collecting phenotypic data, which is crucial for monitoring plant growth trajectories and detecting pests and diseases, continues to be a labor-intensive endeavor. Technological advances have enabled an efficient collection of three-dimensional (3D) data, yet this process currently involves a set of intricate steps. Therefore, the development of an effective phenotyping method is essential. In this study, we developed a phenotyping process based on 3D reconstruction, including mask image generation using deep neural network models, 3D reconstruction using the Structure from Motion/Multi-View Stereo (SfM/MVS) pipeline, and leaf surface reconstruction for leaf area estimation. Our investigation using soybean datasets into the optimal magnification for input images in mask generation models revealed that a 1/5.4× magnification was most effective for segmenting thin structures. Using mask images in the SfM/MVS pipeline limited the region of interest, and this could decrease the processing time and improve the quality of the point-cloud data. We assessed four scenarios regarding mask image usage and found that the scenario that set the mask images of soybeans and stages before SfM and soybeans only after SfM yielded the highest-quality point-cloud data and was the second fastest in processing. Finally, we compared the Poisson reconstruction and B-spline surface fitting for leaf surface reconstruction from point clouds. B-spline fitting shows a greater correlation with destructive measurements. We proposed an optimal workflow for estimating leaf area based on these results. Additionally, to contribute to the development of plant phenotyping methods, we provided a web application for mask generation, a command-line tool for leaf surface reconstruction, and validation datasets.
Modeling Molecular Mechanisms of Pirfenidone Interaction with Kinases
Authors: Wijewardhane Prageeth R. , Wells Adrienne , Muhoberac Matthew , Leung Kai P. , Chopra Gaurav
Published: March 2024

Scar formation is a process that occurs due to increased collagen deposition and uncontrolled inflammation. Previous studies have demonstrated that Pirfenidone (Pf), an FDA approved anti-inflammatory and anti-fibrotic drug can reduce inflammationin vivoas well as regulate activation of LPS-stimulated neutrophils. However, the molecular level mechanism of Pf’s action is not well understood. Here, we used neural networks to identify new targets and molecular modeling methods to investigate the Pf’s action pathways at the molecular level that are related to its ability to reduce both the inflammatory and remodeling phases of the wound healing process. Out of all the potential targets identified, both molecular docking and molecular dynamics results suggest that Pf has a noteworthy binding preference towards the active conformation of the p38 mitogen activated protein kinase-14 (MAPK14) and it is potentially a type I inhibitor-like molecule. In addition to p38 MAPK (MAPK14), additional potential targets of Pf include AKT1, MAP3K4, MAP2K3, MAP2K6, MSK2, MAP2K2, ERK1, ERK2, and PDK1. We conclude that several proteins/kinases, rather than a single target, are involved in Pf’s wound healing ability to regulate signaling, inflammation, and proliferation.
Unveiling lipid chemodiversity in root exudates: A comprehensive characterization of the exudate metabo-lipidome in a perennial grass
Authors: Couvillion Sneha P. , Yang Isabella H. , Hermosillo Dylan , Eder Josie , Bell Sheryl , Hofmockel Kirsten S.
Published: March 2024

The rhizosphere, where plant roots meet soil, is a hub of biogeochemical activity with ecosystem impacts on carbon stocks. Root derived carbon has been found to contribute more to soil carbon stocks than aboveground litter. Nonetheless, the molecular chemodiversity of root exudates remains poorly understood due to limited characterization and annotation. Here our goal was to discover the molecular chemodiversity of metabolites and lipids in root exudates to advance our understanding of plant root inputs belowground. We worked with mature, field-grown tall wheatgrass (Thinopyrum ponticum) and optimized exudate collection protocols to enable the capture of non-polar lipids in addition to polar and semi-polar metabolites. Rates of carbon input via hydrophobic exudates were approximately double that of aqueous exudates and carbon/nitrogen ratios were markedly higher in hydrophobic compared to aqueous exudates, emphasizing the importance of lipids, due to their high carbon content. To maximize molecular coverage of exudate chemodiversity, we used liquid chromatography coupled tandem mass-spectrometry for paired untargeted metabolomics and lipidomics or ‘metabo-lipidomics’. We substantially increased the characterization of exudate chemodiversity by employing both tandem mass spectral library searching and deep learning-based chemical class assignment. Notably, in this unprecedented characterization of intact lipids in root exudates, we discovered a diverse variety of lipids, including substantial levels of triacylglycerols (∼19 μg/g fresh root per min), fatty acyls, sphingolipids, sterol lipids, and glycerophospholipids. Comparison of the root exudate and tissue lipidomes revealed minimum glycerophospholipids in exudates, suggesting the exudate protocol did not extract lipids from root cell membranes.
An atlas ofBrachypodium distachyonlateral root development
Authors: De Jesus Vieira Teixeira Cristovao , Bellande Kevin , van der Schuren Alja , O’Connor Devin , Hardtke Christian S. , Vermeer Joop EM
Published: March 2024

The root system of plants is a vital part for successful development and adaptation to different soil types and environments. Besides allowing exploration of the soil for water and nutrients, it also provides anchorage. A major determinant of the shape of a plant root system is the formation of lateral roots, allowing for expansion of the root system.Arabidopsis thaliana, with its simple root anatomy, has been extensively studied to reveal the genetic program underlying root branching. However, to get a more general understanding of lateral root development, comparative studies in species with a more complex root anatomy are required.Brachypodium distachyonis a wild, temperate grass species, that is related to important crops such as wheat. Its roots contain multiple cortex layers and an exodermis that functions as an additional root barrier, besides the endodermis. Here, by combining optimized clearing methods and histology, we describe an atlas of lateral root development in Brachypodium. We show that lateral roots initiate from enlarged phloem pole pericycle cells and that the overlying endodermis reactivates its cell cycle and eventually forms the root cap. In addition, auxin signaling reported by the DR5 reporter was not detected in the phloem pole pericycle cells or young primordia. In contrast, auxin signaling was activated in the overlying cell cortical layers, including the exodermis. Thus, Brachypodium is a valuable model to investigate how signaling pathways and cellular responses have been repurposed to facilitate lateral root organogenesis.
Quantum mechanical-like approach with non-Hermitian effective Hamiltonians in spin-orbit coupled optical cavities
Authors: Oliwa Przemysław , Bardyszewski Witold , Szczytko Jacek
Published: March 2024

We present a comprehensive analytical model of resonant states in birefringent microcavities with permeable mirrors. We derive an effective, non-Hermitian photonic Hamiltonian describing cavity mode dispersion and modal lifetimes by applying the Green's function technique based on the Mittag-Leffler expansion with respect to the resonant states and the k·p perturbation theory known from semiconductor physics. Using this formalism we obtained results which can be interpreted as effective cavity mode spin-orbit coupling. We use this method to derive the two-mode Hamiltonian to describe the properties of light in the cavity, which significantly reduces the computational effort and properly captures the polarization of the eigenmodes. This is done by introducing the necessary corrections to the Hamiltonian matrix and modifying the basis modes resulting from the coupling with other optical modes present in the system. This simplified Hamiltonian allows us to determine the positions of exceptional points in momentum space. These points are connected by Fermi arcs and appear due to non-Hermiticity and PT symmetry.

Published by the American Physical Society
2024
Uncovering the role of principals in enhancing teacher professional learning in a centralized education system
Authors: Abbaspour Fatemeh , Hosseingholizadeh Rezvan , Bellibaş Mehmet Şükrü
Published: March 2024

Purpose

Current school leadership research has primarily utilized quantitative methods to explore the relationship between leadership and teacher learning. However, there is a notable gap in understanding how principals facilitate professional learning, especially in centralized educational settings. This study aims to address this gap by examining the role of school leadership in enhancing teacher professional learning within a highly centralized education system.

Design/methodology/approach

This qualitative case study delves into the lived experiences of 15 teachers and eight school leaders in eight primary schools in Mashhad, Iran. Through semistructured interviews, researchers employed open and axial coding to systematically explore and categorize qualitative data. The study focuses on understanding the role of principal leadership in facilitating teacher professional learning by connecting themes and sub-themes across transcripts.

Findings

Effective principals worked on the cultivation of a culture that champions perpetual personal growth and development, the nurturing of a collaborative learning community, and the provision of essential resources and support. Findings showed the pivotal role of principals in promoting teachers' self-development, facilitating idea exchange and acknowledging their efforts. Principals appeared as key to encouraging information sharing, fostering collective learning, promoting professional development, overseeing teaching practices and ensuring the availability of resources to cultivate a supportive climate in a centralized education context.

Originality/value

We concluded that in centralized education, leadership practices for promoting teacher learning share similarities and differences with decentralized settings. The findings offer guidance for principals in centralized systems, supporting them in facilitating teacher professional learning in their schools.
Does public debt moderate government spending – informal economy nexus? Evidence from the Asian countries
Authors: Tran Pham Toan Khanh , Nguyen Le Quyen Hoang Thuy To
Published: March 2024

Purpose

The purpose of this study is to explore the relationship between government spending, public debt and the informal economy. In addition, this paper investigates the moderating role of public debt in government spending and the informal economy nexus.

Design/methodology/approach

By utilizing a data set spanning from 2000 to 2017 of 32 Asian economies, the study has employed the dynamic ordinary least squares (DOLS) and fully modified ordinary least squares (FMOLS). The study is also extended to consider the marginal effects of government spending on the informal economy at different degrees of public debt.

Findings

The results indicate that an increase in government spending and public debt leads to an expansion of the informal economy in the region. Interestingly, the positive effect of government spending on the informal economy will increase with a rise in public debt.

Originality/value

This study stresses the role of government spending and public debt on the informal economy in Asian nations. To the best of the authors' knowledge, this study pioneers to explore the moderating effect of public debt in the public spending-informal economy nexus.
Adapting to discontinuous technological change from the perspective of knowledge management: a case study from the lighting industry in Lin’an, China
Authors: Li Zhengwei , Li Wenxin , Carusone Rosalinda , Profita Sofia
Published: March 2024

Purpose

This study aims to answer the question of how incumbent firms cultivate dynamic capabilities through knowledge management so that they can efficiently adapt to the changing external environment.

Design/methodology/approach

This study adopts a case study approach and collects data through interviews and secondary public information on the lighting industry and two lighting firms in Lin'an, China. It qualitatively examines the challenges and strategic recommendations for incumbent firms in the context of discontinuous technological change from a knowledge management perspective.

Findings

Incumbent firms often face a variety of challenges when responding to discontinuous technological change. These challenges include identifying opportunities, overcoming path dependence and dealing with employee resistance to change. To overcome these difficulties, three strategies have been proposed to enhance the dynamic capabilities of incumbent firms through knowledge management: cross-border search helps firms improve their knowledge acquisition capabilities and better understand their environment to identify opportunities; building strategic leadership overcomes path dependence and improves knowledge integration capabilities; organizational learning deepens employees’ understanding of change and enhances organizational knowledge application capabilities.

Research limitations/implications

Previous research attributes a firm's ability to cope with discontinuous technological change solely to its general resources, which weakens the importance of knowledge management in this context. This study emphasizes the importance of knowledge as a crucial strategic resource in developing the essential dynamic capabilities for incumbent firms to cope with discontinuous technological change.

Practical implications

This study provides an in-depth analysis of incumbent firms' coping strategies in the new context of discontinuous technological change and further promotes cross-disciplinary research.

Originality/value

This study provides an in-depth analysis of coping strategies in the new context of discontinuous technological change, furthermore theoretically advancing the interdisciplinary research of firm transformation and knowledge management. Meanwhile, it is crucial to identify the preconditions for cultivating dynamic capabilities, especially from a knowledge-based view, which enhances the depth of knowledge management research.
The efficacy of psychoeducation to improve personal skills and well-being among health-care professionals returning to clinical practice: a pilot pre-post study
Authors: Szekely Raul , Mazreku Syrgena , Bignell Anita , Fadel Camilla , Iannelli Hannah , Vega Marta Ortega , O'Sullivan Owen P. , Tiley Claire , Attoe Chris
Published: March 2024

Purpose

Many health-care professionals leave clinical practice temporarily or permanently. Interventions designed to facilitate the return of health-care professionals fail to consider returners’ psychosocial needs despite their importance for patient care. This study aims to evaluate the efficacy of a psychoeducational intervention in improving personal skills and well-being among UK-based health-care professionals returning to clinical practice.

Design/methodology/approach

In total, 20 health-care professionals took part in the one-day intervention and completed measures of demographics, self-efficacy, positive attitudes towards work and perceived job resources before and after the intervention. A baseline comparison group of 18 health-care professionals was also recruited.

Findings

Significant associations were detected between return-to-work stage and study group. Following the intervention, participants reported improvements in self-efficacy and, generally, perceived more job resources, whereas positive attitudes towards work decreased. While none of these changes were significant, the intervention was deemed acceptable by participants. This study provides modest but promising evidence for the role of psychoeducation as a tool in supporting the psychosocial needs of returning health-care professionals.

Research limitations/implications

Additional research is needed to clarify the reliability of intervention effects, its effectiveness compared to alternative interventions, and the impact across different subgroups of returning health-care professionals.

Practical implications

Return-to-practice interventions should address the psychosocial needs of health-care professionals in terms of their personal skills and well-being. Psychoeducation can increase self-efficacy and perceptions of job resources among returning health-care professionals.

Originality/value

This study sheds light on a relatively understudied, but fundamental area – the psychosocial challenges of health-care professionals returning to clinical practice – and further justifies the need for tailored interventions.
The information needs of users in the metaverse communities: a grounded theory study
Authors: Guo Yajun , Ma Huifang , Zhou Jiahua , Chen Yanchen , Yuan Yiming
Published: March 2024

Purpose

This article aims to understand users' information needs in the metaverse communities and to analyze the similarities and differences between their information needs and those of users in Internet communities.

Design/methodology/approach

This study conducted semi-structured interviews with users in the metaverse communities to gather raw data. Grounded theory research methods were employed to code and analyze the collected interview data, resulting in the extraction of 40 initial concepts, 15 subcategories and 5 main categories. Based on Maslow’s hierarchy of needs theory, this paper constructs the hierarchical model of users' information needs in the metaverse communities. It compares the differences between users' information needs in the metaverse and Internet fields.

Findings

The user’s information needs in the metaverse communities are divided into two types: deficiency needs and growth needs. Deficiency needs have two levels. The first level is the demand for basic information resources. The second level is the users demand for information assistance. Growth needs have three levels. The first level is the need for information interactions. The second level is the need for community rules. The ownership information in the community rules can provide proof of user status, assets and so on. The third level is the need for users to contribute and share their own created information content.

Originality/value

This article presents the latest research data from in-depth interviews with users in the metaverse communities. It aims to help builders and managers of metaverse communities understand users' information needs and improve the design of virtual communities.
Comparison of elastic anisotropy in the Middle and Upper Wolfcamp Shale, Midland Basin
Authors: Sayers Colin M. , Dasgupta Sagnik
Published: March 2024

Organic‐rich shales contain large amounts of oil and gas and are anisotropic because of fine‐scale layering and the partial alignment of organic matter and anisotropic clay minerals with the bedding. An example is the Wolfcamp Shale in the Permian Basin. Elastic anisotropy needs to be accounted for in the characterization of such formations using seismic data and plays a role in hydraulic fracturing and in the evaluation of stress changes and geomechanical effects resulting from production. Using extensive well log data acquired in the Midland Basin, the eastern sub‐basin of the Permian Basin, we estimate and compare the elastic anisotropy in the Middle and Upper Wolfcamp Shale by combining data from a vertical pilot well with two lateral wells, one (6SM) drilled in the Middle Wolfcamp and one (6SU) drilled in the Upper Wolfcamp. The data used were acquired at the Hydraulic Fracture Test Site 1, located in the eastern part of the Midland Basin. Thomsen's anisotropy parameter calculated from the fast and slow shear sonic is higher on average for the 6SM lateral than for 6SU, consistent with there being less carbonate content in 6SM than in 6SU. However, the anisotropy parameter in some regions with higher carbonate content in well 6SU is higher than in well 6SM. This may indicate the influence of natural fractures. The primary set of steeply dipping fractures observed in the lateral wells at Hydraulic Fracture Test Site 1 acts to increase if the ratio of the normal‐to‐shear fracture compliance is less than about 0.5. Sub‐horizontal fractures may also increase and could affect the vertical extent of hydraulic fractures. Relations between elastic moduli C33 and C55 in the Upper and Lower Wolfcamp in a vertical pilot well allow C33 to be predicted in a lateral well using measurements of C55 in that well. Comparison of Thomsen's anisotropy parameters and , with calculated from the measured values of C55 and C66 and calculated from the measured values of C11 and predicted values of C33, show that  is mostly greater than .