bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creating saponin‐free yellow pea seeds by CRISPR/Cas9‐enabled mutagenesis on β‐amyrin synthase
Authors: Hodgins Connor L. , Salama Eman M. , Kumar Rahul , Zhao Yang , Roth Susan A. , Cheung Irene Z. , Chen Jieyu , Arganosa Gene C. , Warkentin Thomas D. , Bhowmik Pankaj , Ham Byung‐Kook , Ro Dae‐Kyun 
Published: January 2024

AbstractDry pea (Pisum sativum) seeds are valuable sources of plant protein, dietary fiber, and starch, but their uses in food products are restricted to some extent due to several off‐flavor compounds. Saponins are glycosylated triterpenoids and are a major source of bitter, astringent, and metallic off‐flavors in pea products. β‐amyrin synthase (BAS) is the entry point enzyme for saponin biosynthesis in pea and therefore is an ideal target for knock‐out using CRISPR/Cas9 genome editing to produce saponin deficient pea varieties. Here, in an elite yellow pea cultivar (CDC Inca), LC/MS analysis identified embryo tissue, not seed coat, as the main location of saponin storage in pea seeds. Differential expression analysis determined that PsBAS1 was preferentially expressed in embryo tissue relative to seed coat and was selected for CRISPR/Cas9 genome editing. The efficiency of CRISPR/Cas9 genome editing of PsBAS1 was systematically optimized in pea hairy roots. From these optimization procedures, the AtU6‐26 promoter was found to be superior to the CaMV35S promoter for gRNA expression, and the use of 37°C was determined to increase the efficiency of CRISPR/Cas9 genome editing. These promoter and culture conditions were then applied to stable transformations. As a result, a bi‐allelic mutation (deletion and inversion mutations) was generated in the PsBAS1 coding sequence in a T1 plant, and the segregated psbas1 plants from the T2 population showed a 99.8% reduction of saponins in their seeds. Interestingly, a small but statistically significant increase (~12%) in protein content with a slight decrease (~5%) in starch content was observed in the psbas1 mutants under phytotron growth conditions. This work demonstrated that flavor‐improved traits can be readily introduced in any pea cultivar of interest using CRISPR/Cas9. Further field trials and sensory tests for improved flavor are necessary to assess the practical implications of the saponin‐free pea seeds in food applications.
Mycorrhizal communities of Vanilla planifolia in an introduction area (La Réunion) under varying cultivation practices
Authors: Petrolli Rémi , Selosse Marc‐André , Bonillo Céline , Griveau Chantal , Lalanne‐Tisné Guillaume , Comes Bertrand , Kodja Hippolyte , Martos Florent 
Published: January 2024

Societal Impact StatementVanilla is one of the most valuable spices in the world. In Madagascar and La Réunion, the world's leading producers, vanilla is of great economic and cultural importance. Like all orchids, vanilla plants associate with mycorrhizal fungi in their roots forming mutualistic associations that allow them to grow and thrive. Understanding the diversity of mycorrhizal fungi adapted to vanilla cultivation, particularly in the Indian Ocean islands where they have never previously been studied, is becoming a necessity for maintaining vanilla crops in these regions in the face of climate change and the emergence of new pathogens.Summary

The vanilla orchid (Vanilla spp.) is one of the most valuable cultivated plants worldwide. As with all orchids, vanillas form mycorrhizal associations with fungi in their roots, but their fungal partners have not been investigated outside their native geographic range in Central America.
We investigated the whole fungal and mycorrhizal associations in cultivated vanilla (Vanilla planifolia) by sequencing the fungal ITS‐2 marker in the terrestrial and aerial roots using a metabarcoding approach. We selected plants cultivated in three conditions (i.e., cultivation under shade house, in openfield, or in the understory) in one locality of La Réunion island (Indian Ocean) and tested for a possible effect of cultivation practices on fungal communities.
Cultivated vanillas in La Réunion mainly associate with Tulasnellaceae (75 OTUs) and Ceratobasidiaceae (8 OTUs). Among the seven most abundant Tulasnellaceae, six are similar to fungi detected in the roots of cultivated vanillas in Central America or in the roots of native orchids in La Réunion. Cultivation practices impacted both total fungal and mycorrhizal community compositions with no clear effect on fungal richness. Notably, Tulasnellaceae and Ceratobasidiaceae were scarce in aerial roots, except in the traditional cultivation in the forest understory.
These results shed light on the geographical origins of mycorrhizal fungi of cultivated vanillas in La Réunion and show that they form a pool of both locally and globally distributed fungal partners. These mycorrhizal communities vary according to cultivation practices, and their potential roles in plant nutrition and resistance against pathogens await further attention.
Conservation agrivoltaics for sustainable food‐energy production
Authors: Time Alson , Gomez‐Casanovas Nuria , Mwebaze Paul , Apollon Wilgince , Khanna Madhu , DeLucia Evan H. , Bernacchi Carl J. 
Published: January 2024

Societal Impact StatementTransformative agricultural strategies like agrivoltaics (AV) are essential for addressing the pressing global issues of sustainable energy and food production in a changing climate. Conservation‐agrivoltaics (Conservation‐AV) provides the potential to meet these needs while reinforcing natural resources and protecting the environment. It could enhance the ecological benefits of AV by improving soil health and biodiversity. It could create economic opportunities for farmers and increase the resilience and diversity of food crops under changing climate conditions. Furthermore, it could inform stakeholders about the benefits and challenges of implementing conservation agriculture management practices (CAMP) in AV and encourage further exploration and adoption of this innovative approach.SummaryTransformative strategies in agriculture are needed to address urgent global challenges related to energy and food production while reinforcing natural resources and the environment. Agrivoltaics (AV) has emerged in the past decade as one solution to this fundamental challenge of improving energy and food security. AV is defined as the co‐location of solar photovoltaic (PV) panels and crops on the same land to optimize food and energy production simultaneously and sustainably. Here, we propose that AV, together with conservation agriculture management practices (CAMP) strategies can help to intensify food security and energy production while reinforcing natural resources and the environment. Our main assertions in this opinion article are that: (1) AV systems need to overcome several agronomical, environmental, and ecological challenges to intensify food and energy production sustainably; (2) CAMP applied to AV systems can preserve the environment and ensure climate‐resilient food production; (3) implementation of CAMP in AV can lead to long‐term carbon sequestration, lower greenhouse gas emissions, and maintain or increase crop yields while preserving soil health and biodiversity; and (4) adoption of CAMP in AV can bring economic benefits, although challenges need to be overcome. This opinion article proposes a new ecosystem approach to integrate renewable energy and sustainable food production and encourages research on the effects of CAMP on AV systems.
Imaging of pulmonary fibrosis in children: A review, with proposed diagnostic criteria
Authors: DeBoer Emily M. , Weinman Jason P. , Ley‐Zaporozhan Julia , Griese Matthias , Deterding Robin , Lynch David A. , Humphries Stephen M. , Jacob Joseph 
Published: January 2024

AbstractComputed tomography (CT) imaging findings of pulmonary fibrosis are well established for adults and have been shown to correlate with prognosis and outcome. Recognition of fibrotic CT findings in children is more limited. With approved treatments for adult pulmonary fibrosis, it has become critical to define CT criteria for fibrosis in children, to identify patients in need of treatment and those eligible for clinical trials. Understanding how pediatric fibrosis compares with idiopathic pulmonary fibrosis and other causes of fibrosis in adults is increasingly important as these patients transition to adult care teams. Here, we review what is known regarding the features of pulmonary fibrosis in children compared with adults. Pulmonary fibrosis in children may be associated with genetic surfactant dysfunction disorders, autoimmune systemic disorders, and complications after radiation, chemotherapy, transplantation, and other exposures. Rather than a basal‐predominant usual interstitial pneumonia pattern with honeycombing, pediatric fibrosis is primarily characterized by reticulation, traction bronchiectasis, architectural distortion, or cystic lucencies/abnormalities. Ground‐glass opacities are more frequent in children with fibrotic interstitial lung disease than adults, and disease distribution appears more diffuse, without clearly defined axial or craniocaudal predominance. Following discussion and consensus amongst a panel of expert radiologists, pathologists and physicians, distinctive disease features were integrated to develop criteria for the first global Phase III trial in children with pulmonary fibrosis.
Screening of novel biomarkers for acute kidney transplant rejection using DIA‐MS based proteomics
Authors: Wang Ce , Feng Gang , Zhao Jie , Xu Yang , Li Yang , Wang Lin , Wang Meng , Liu Miao , Wang Yilin , Mu Hong , Zhou Chunlei 
Published: January 2024

AbstractBackgroundKidney transplantation is the preferred treatment for patients with end‐stage renal disease. However, acute rejection poses a threat to the graft long‐term survival. The aim of this study was to identify novel biomarkers to detect acute kidney transplant rejection.MethodsThe serum proteomic profiling of kidney transplant patients with T cell‐mediated acute rejection (TCMR) and stable allograft function (STA) was analyzed using data‐independent acquisition mass spectrometry (DIA‐MS). The differentially expressed proteins (DEPs) of interest were further verified by enzyme‐linked immunosorbent assay (ELISA).ResultsA total of 131 DEPs were identified between STA and TCMR patients, 114 DEPs were identified between mild and severe TCMR patients. The verification results showed that remarkable higher concentrations of serum amyloid A protein 1 (SAA1) and insulin like growth factor binding protein 2 (IGFBP2), and lower fetuin‐A (AHSG) concentration were found in TCMR patients when compared with STA patients. We also found higher SAA1 concentration in severe TCMR group when compared with mild TCMR group. The receiver operating characteristics (ROC) analysis further confirmed that combination of SAA1, AHSG, and IGFBP2 had excellent performance in the acute rejection diagnosis.ConclusionsOur data demonstrated that serum SAA1, AHSG, and IGFBP2 could be effective biomarkers for diagnosing acute rejection after kidney transplantation. DIA‐MS has great potential in biomarker screening of kidney transplantation.
A novel indicator for temperature control in heat stroke treatment
Authors: Feng Jian , Tang Mingyang , Gong Meiting , Li Fuxiang , Li Yunming , Huang Bo , Feng Fan , Wang Xiong , Pei Haifeng 
Published: January 2024

AbstractBackgroundTemperature control plays a pivotal role in patients with heat stroke (HS), but little work has been done sufficiently on the use of temperature control to reflect disease progression. Here, we defined and analyzed the concrete role of controlling time for core temperature to physiological level (CTTP), in order to explore a potential index to guide the treatment of HS.MethodThis is a retrospective cohort study. From three hospitals located in Sichuan province, China, we collected a total of 179 HS cases with clinical diagnosis and treatment records. We defined CTTP as the time interval of HS onset to stabilization of core temperature (rectal temperature) below 37.7°C and analyzed the correlation between CTTP and inpatient death of HS patients.ResultsOf all the cases, 64.80% were male and 53.07% were exertional heat stroke (EHS). The median (IQR) age was 59 (23.5–73) years old, and the median (IQR) onset temperature was 42 (40.4–42)°C. Multivariable analysis demonstrated significantly high inpatient death in the highest CTTP tertile (>18 h) (hazard ratio: 18.75; 99% confidence interval: 4.06–86.59; p = .0002). In addition, compared with patients in lowest CTTP tertile, patients in highest CTTP tertile were at significantly higher risk of organ damage: 3.48‐fold for respiratory failure (95% CI: 1.41–8.59, p = .0069); 3.18‐fold for shock (95% CI: 1.37–7.39, p = .0071); 4.09‐fold for rhabdomyolysis (95% CI: 1.73–9.64, p = .0013); 4.64‐fold for renal damage (95% CI: 2.12–10.14, p = .0001).ConclusionLong of CTTP predicts inpatient death of HS patients with a CTTP tertile >18 h associated with the highest rate of inpatient death.
A study on the efficacy and safety of aprepitant injection in preventing and treating nausea and vomiting induced by platinum‐based chemotherapy in lung cancer
Authors: Fei Yan , siwen Liu , xiaoyou Li , Xiaoyue Xu , Yuan Wu , Bo Shen 
Published: January 2024

AbstractThis study aimed to assess the clinical efficacy and safety of aprepitant injection in preventing and treating nausea and vomiting induced by platinum‐based chemotherapy in lung cancer patients. Forty‐eight patients with advanced first‐line lung cancer undergoing cisplatin‐ or carboplatin‐based chemotherapy were randomly assigned to either the experimental group or the control group, with 24 patients in each group. The control group received dexamethasone and palonosetron for vomiting prevention, whereas the experimental group received dexamethasone, palonosetron, and aprepitant injection. The study compared the incidence of acute and delayed vomiting, functional life index (FLIE) scores for nausea and vomiting at 24 and 120 h postchemotherapy and the occurrence of adverse drug reactions between the two groups. The effective control rate of acute‐phase vomiting in the treatment group was 83.33%, significantly higher than 45.83% in the control group, with a statistically significant difference (p < .05). The treatment group also demonstrated a higher effective control rate of delayed vomiting, with 75% compared with 41.67% in the control group, which was statistically significant (p < .05). Furthermore, FLIE scores in the treatment group at 24 and 120 h after chemotherapy were higher compared with the control group, with a statistically significant difference (p < .05). The incidence of complications such as fatigue, headache, dyspepsia, anorexia, hiccup, and constipation showed no significant difference between the two groups (p > .05). Aprepitant injection effectively prevents platinum‐based chemotherapy‐induced nausea and vomiting, enhances patients' quality of life, and demonstrates good safety, justifying its clinical adoption.
Metabolic analysis using HR‐MAS in prostate tissue for prostate cancer diagnosis
Authors: Panach‐Navarrete Jorge , González‐Marrachelli Vannina , Morales‐Tatay José Manuel , García‐Morata Francisco , Sales‐Maicas María Ángeles , Monleón‐Salvado Daniel , Martínez‐Jabaloyas José María 
Published: January 2024

AbstractIntroductionIn this study we used nuclear magnetic resonance spectroscopy in prostate tissue to provide new data on potential biomarkers of prostate cancer in patients eligible for prostate biopsy.Material and MethodsCore needle prostate tissue samples were obtained. After acquiring all the spectra using a Bruker Avance III DRX 600 spectrometer, tissue samples were subjected to routine histology to confirm presence or absence of prostate cancer. Univariate and multivariate analyses with metabolic and clinical variables were performed to predict the occurrence of prostate cancer.ResultsA total of 201 patients, were included in the study. Of all cores subjected to high‐resolution magic angle spinning (HR‐MAS) followed by standard histological study, 56 (27.8%) tested positive for carcinoma. According to HR‐MAS probe analysis, metabolic pathways such as glycolysis, the Krebs cycle, and the metabolism of different amino acids were associated with presence of prostate cancer. Metabolites detected in tissue such as citrate or glycerol‐3‐phosphocholine, together with prostate volume and suspicious rectal examination, formed a predictive model for prostate cancer in tissue with an area under the curve of 0.87, a specificity of 94%, a positive predictive value of 80% and a negative predictive value of 84%.ConclusionsMetabolomics using HR‐MAS analysis can uncover a specific metabolic fingerprint of prostate cancer in prostate tissue, using a tissue core obtained by transrectal biopsy. This specific fingerprint is based on levels of citrate, glycerol‐3‐phosphocholine, glycine, carnitine, and 0‐phosphocholine. Several clinical variables, such as suspicious digital rectal examination and prostate volume, combined with these metabolites, form a predictive model to diagnose prostate cancer that has shown encouraging results.
Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory
Authors: Bairagya Hridoy R. , Tasneem Alvea , Sarmadhikari Debapriyo 
Published: January 2024

AbstractThe new viral strains of severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) are continuously rising, becoming more virulent, and transmissible. Therefore, the development of new antiviral drugs is essential. Due to its significant role in the viral life cycle of SARS‐CoV‐2, the main protease (Mpro) enzyme is a leading target for antiviral drug design. The Mpro monomer consists of domain DI, DII, and DI‐DII interface. Twenty‐one conserved water molecules (W4–W24) are occupied at these domains according to multiple crystal structure analyses. The crystal and MD structures reveal the presence of eight conserved water sites in domain DI, DII and remaining in the DI‐DII interface. Grid‐based inhomogeneous fluid solvation theory (GIST) was employed on MD structures of Mpro native to predict structural and thermodynamic properties of each conserved water site for focusing to identify the specific conserved water molecules that can easily be displaced by proposed ligands. Finally, MD water W13 is emerged as a promising candidate for water mimic drug design due to its low mean interaction energy, loose binding character with the protein, and its involvement in a water‐mediated H‐bond with catalytic His41 via the interaction Thr25(OG)‐‐‐W13‐‐‐W‐‐‐His41(NE2). In this context, water occupancy, relative interaction energy, entropy, and topologies of W13 are thermodynamically acceptable for the water displacement method. Therefore, the strategic use of W13's geometrical position in the DI domain may be implemented for drug discovery against COVID disease by designing new ligands with appropriately oriented chemical groups to mimic its structural, electronic, and thermodynamic properties.
Modulating opto‐electronic and magnetic responses of Mo‐ and Zn‐adsorbed LiNbO3 (1 1 1) surface for advanced energy harvesting applications: A comprehensive study
Authors: Rafiq Qaiser , Khan Muhammad Tahir , Azam Sikander , ur Rahman Amin , Hayat Sardar Sikandar , Alanazi Yousef Mohammed , Ahmad Syed Sheraz 
Published: January 2024

AbstractThis study aimed to comprehensively investigate the optoelectronic and magnetic properties of Mo, Zn/LiNbO3 (1 1 1) material. The primary objectives were to understand the potential for manipulating the material's magnetism and to elucidate the origin of spin‐polarized states and magnetic moments, particularly with respect to the unpaired d orbitals of Nb, Mo, and Zn atoms. To achieve these objectives, we employed the Pardew–Burke–Ernzerhof (PBE) method within the Generalized Gradient Approximation (GGA + U) framework. This computational approach allowed us to examine the optoelectronic and magnetic characteristics of the material in detail. Our research yielded several key findings that enhance our understanding of Mo, Zn/LiNbO3 (1 1 1) material. We observed a modest improvement in the material's absorption capacity within the visible spectrum, accompanied by a discernible red‐shift. Notably, our study involved the calculation of the dielectric function and refractive constant of the material, revealing a strong correlation between absorption trends and the dielectric constant. Furthermore, our investigation uncovered that Mo, Zn/LiNbO3 (1 1 1) exhibits distinct conduction and valence bands, with p and d orbitals predominantly contributing to each, respectively. The energy gap of the material falls within a range of 0.30–1.04 eV. A particularly significant finding was the narrower band gap of Mo, Zn/LiNbO3 (1 1 1) material, which can be attributed to the superposition of Mo‐d and Zn‐p orbit energy levels with O‐p orbit energy levels, ultimately forming a covalent bond. Importantly, our research demonstrated the material's heightened optical absorption within the visible spectrum, suggesting its suitability for various photonic and optoelectronic applications. Additionally, we calculated a wide range of optical characteristics, including the dielectric function, absorption coefficient, energy loss, reflectivity, refractive index, extinction coefficient, and optical conductivity, providing a comprehensive assessment of the material's optical properties.
Predictor‐based continuous‐discrete nonlinear observer design subject to aperiodic sampled and delayed measurement
Authors: Zhuang Xincheng , Wang Haoping , Tian Yang 
Published: January 2024

AbstractIn this paper, a predictor‐based continuous‐discrete nonlinear observer is proposed for a class of nonaffine Lipschitz nonlinear systems with aperiodic sampled delayed output measurements and external disturbance. Firstly, this study introduces a class of delayed sampling hybrid nonlinear systems. By employing Lyapunov techniques and trajectory‐based stability theory, sufficient conditions are established for ensuring input‐to‐state stability of the delayed sampling hybrid nonlinear system with respect to external disturbances. Then the predictor‐based continuous‐discrete nonlinear observer is designed which consists of a continuous‐time observer, a compensating injector and a predictor. The continuous‐time observer is utilized to obtain continuous and delay‐free state estimation. The compensating injector is designed to compensate for output errors that occur between sampling instants. Furthermore, the predictor is employed to obtain delay‐free output error information, which is then utilized by the continuous‐time observer for feedback correction. The proposed observer's exponential input‐to‐state property against the disturbance is proved via the proposed hybrid system stability theory. The effectiveness of the proposed observers has been demonstrated through numerical simulations and performance comparisons with the zero‐order holder‐based observer and the output predictor‐based observer designs in order to highlight the effectiveness and advantages of the proposed observer.