bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Identification of Phytotoxins Produced by Glomerella cingulata Using High‐Resolution Mass Spectrometry‐Based Qualification, Targeted Structural Confirmation and Their Characteristics Investigation
Authors: Yu Xin , Liu Zhiyang , Zhang Huidi , Wang Caixia , Lian Sen , Dong Xiangli , Li Baohua , Li Pingliang 
Published: September 2024

ABSTRACTGlomerella cingulata is a pathogenic fungus that can cause apple Glomerella leaf spot (GLS), a new and destructive apple disease in China. Phytotoxins are important factors closely related to the disease process, but there is still no report on the phytotoxins of G. cingulata. The aim of this study was to rapidly identify the phytotoxins of this pathogen using a strategy of HRMS‐based preliminary qualification, followed by targeted structure confirmation and also investigation of phytotoxicity characteristics. First, the crude toxin sample was directly analyzed by the UPLC‐HRMS and GC‐MS, and the data were processed to screen for possible phytotoxic compounds using MS library and the phytotoxicity‐related literature. The reference standards of credible phytotoxic compounds were then subjected to targeted structure validation (signal comparison between standards and compounds in crude toxin via HPLC‐DAD, UPLC‐MS/MS, and GC‐MS), and also the phytotoxicity assay. The results confirmed six phytotoxins produced by G. cingulata, namely 5‐hydroxymethyl‐2‐furancarboxylic acid (HMFCA), 2,5‐bis(hydroxymethyl)furan (BHMF), 2‐furoic acid (FA), 2,3‐butanediol, trans‐aconitic acid (TAA), and cis‐aconitic acid (CAA). Of these, HMFCA and TAA exhibited greater phytotoxicity. Main characteristics: All of them were non‐host‐selective toxins, and toxins were synergistically phytotoxic to the host when mixed. BHMF, HMFCA, FA, TAA, and CAA could be commonly produced by all tested strains, and their phytotoxicity can be significantly inhibited or even eliminated at high temperatures or high pH. The elucidation of the phytotoxins of G. cingulata in this work could provide information on the pathogenesis and control of apple GLS.
Assessing the separate contribution of the domain, RCM and GCM to the uncertainty in CORDEX simulations over the overlapped regions that include Jordan
Authors: Alkhasoneh Hebah , Rowe Clinton 
Published: September 2024

AbstractThe Coordinated Regional Downscaling Experiment (CORDEX) offers a framework for regional climate downscaling experiments over continental‐based domains that overlap; this allows for conducting multimodel analysis. However, a question is raised about the uncertainty due to domain selection. This study aims to evaluate the sensitivity of CORDEX simulations to the choices of domain, downscaling regional climate model (RCM) and driving global model (GCM) over a Middle East study region, including Jordan. Understanding these sensitivities helps assess simulation uncertainties and enhance regional climate change projections. Taylor diagrams and variance decomposition analyses were used to analyse seasonal temperature and precipitation climatologies. The results indicate that the domain contribution to variance is negligible, whereas the choice of GCM and RCM strongly influences simulations. Variance in temperature is significantly impacted by the driving model (GCM), whereas RCM has a higher influence on precipitation, which reflects their large‐scale versus local nature. The results of this study support the development of multidomain ensembles since projections produced by the same GCM–RCM model combination are consistent across different overlapping domains. On the other hand, this approach facilitates the consideration as well as a comprehensive quantification of the uncertainties arising from the utilization of multiple GCMs and RCMs within such an ensemble. This improves the reliability of regional climate information, thus facilitating the development of effective adaptation strategies and mitigation plans.
Conference proceedings: Inaugural meeting of the consortium for autism, genetic neurodevelopmental disorders, and digestive diseases
Authors: Halladay Alycia , Croffie Joseph , Dallman Julia , Grabenstatter Heidi , Holingue Calliope , Madgett Katie , Margolis Kara G. , Motil Kathleen J. , Jimenez‐Gomez Andres , Ferguson Bradley J. , Moshiree Baha , Still Kate , Williams Kent , Upp Gerald Rick , Bennett William 
Published: September 2024

AbstractObjectivesIndividuals with neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD), often experience a higher prevalence of gastrointestinal (GI) symptoms but have complex medical and behavioral comorbidities that make diagnosis and treatment difficult. A multi‐stakeholder conference was convened to (a) determine patient and family experiences related to GI symptoms in NDDs, (b) review the clinicians' and researchers' perspectives, and (c) determine actionable steps for future research.MethodsThe Consortium for Autism, Neurodevelopmental Disorders and Digestive Diseases (CANDID; www.candidgi.com) virtually over 2 days in 2022 and consisted of four key activities: (1) an electronic family survey to assess underlying NDDs and GI symptoms, (2) a session focused on family perspectives, (3) review current clinical care and research, and (4) discussion to identify key next steps. Survey results were obtained electronically via the REDCap platform, and descriptive statistics were generated. The sessions were recorded, and themes were identified.ResultsThe pre‐conference survey ran for ~2 months and 739 families provided responses, with 634 completing all items. 83% had a child with an NDD under age 18, and most patients were White (85%) and non‐Hispanic (87%). Constipation (80%), GI reflux disease (51%), and bloating (49%) were the most frequently reported symptoms. Families gave unstructured feedback that the measures used in the surveys were often difficult to answer for patients with NDDs or who were nonspeaking. Family and clinical/scientific sessions identified several common themes, including (1) the need for less invasive diagnostic modalities, (2) the need to validate or adapt existing diagnostic measures (e.g., the Rome IV criteria) and outcome assessments, and (3) the need for enhanced attention to parent and caregiver input in treatment plans.ConclusionsThose providing care to children with NDDs, especially those with communication and cognitive challenges, should be aware of the differing needs in this community and consider family perspectives in managing, treating, and measuring GI issues. Future research should focus on adapting or creating diagnostic and research measures for those with NDDs, developing new diagnostic methods to account for diversity in neurodevelopment and communication, and improving methods for family and caregiver engagement in the care of GI disorders.
Conflict between parents, physicians, and healthcare professionals in medical decision‐making: How to address it—A systematic review from the ESPGHAN Ethics Committee
Authors: Roggero Paola , Grima Anne‐Marie , Crespo‐Escobar Paula , Tapsas Dimitrios , Yahav Jacob 
Published: September 2024

AbstractMedical decisions about pediatric gastroenterology pathologies often involve collaboration between the medical team and the family. On occasions, conflict may arise between the individuals involved in decision making (team–family conflict) causing delays in managing a child's health condition. Little is known on the strategies that can be implemented to address such conflicts. Using the systematic review model by McCullough et al., an electronic literature search was conducted using PUBMED databases and SCOPUS. Studies published between 2001 and 2022 were analyzed to identify high‐risk families, the barriers and facilitators involved in the team–family conflict and the circumstances in which healthcare professionals can be ethically justified to override parents' medical decisions and to trigger the state intervention. The present review provides recommendations on the more suitable ways to manage team–family conflict and gives a practical approach using a case vignette.
Individual and combined effects of high‐temperature stress at booting and flowering stages on rice grain quality
Authors: Wang Wei , Xiao Liujun , Mahmood Aqib , Xu Hanwen , Tang Liang , Liu Leilei , Liu Bing , Cao Weixing , Zhu Yan 
Published: September 2024

AbstractBACKGROUNDHigh temperature stress (HTS) has become a serious threat to rice grain quality and few studies have examined the effects of HTS across multiple stages on rice grain quality. In the present study, we conducted 2 years of HTS treatments under three temperature regimes (32/22 °C, 40/30 °C and 44/34 °C) and HTS durations of 2 days and 4 days at three critical stages: booting, flowering, and a combination of booting and flowering. We employed the heat degree days (HDD) metric, which accounts for both the level and duration of HTS, to quantify the relationships between grain quality traits and HTS.RESULTSThe results revealed the diverse effects of HTS on rice grain quality at different stages, durations and temperature levels. HTS significantly (P < 0.05) reduced grain quality, with the highest sensitivities (reduction per 1 °C day−1 increase in HDD) observed at the flowering stage, followed by the combined and booting stages treatments under mild HTS treatment (40/30 °C). However, under extreme HTS treatments (44/34 °C) for 4 days, rice grains subjected to combined HTS treatment experienced complete mortality.CONCLUSIONPre‐exposed to HTS at the booting stage within a certain intensity can alleviate the adverse effects of post‐flowering HTS on grain quality. This provides valuable insights for assessing the potential impact of multiple HTS events on the grain quality under future climate warming. © 2024 Society of Chemical Industry.
Effect of lipid type on betulin‐stabilized water‐in‐oil Pickering emulsion: emulsion properties, in vitro digestion, and betulin bioaccessibility
Authors: Su Shuxian , Liu Yugang , Li Haiyan , Xia Huiping , Li Peiwang , Qin Si , Shi Meng , Guo Shiyin , Zeng Chaoxi 
Published: September 2024

AbstractBackgroundThe Pickering emulsion delivery technique is widely acknowledged for its efficacy in serving as a carrier that can encapsulate functional components effectively. Previous studies have shown significant differences in the stability of Pickering emulsions composed of different oil phases and in the bioaccessibility of the encapsulated functional ingredients. This study therefore investigated the effects of different carrier oils in the betulin self‐stabilized water‐in‐oil (W/O) Pickering emulsion on the stability of the emulsion and bioaccessibility of betulin.ResultsThe results showed that the oil type was one of the main factors affecting the stability of the emulsion. Palm oil and coconut oil provided better storage stability and centrifugal stability due to the high saturated fatty acid content. The bioavailability of betulin correlated significantly with the composition and characteristics of fatty acids in carrier oils. Carrier oils rich in low‐saturation long‐chain fatty acids tended to release more free fatty acids (FFAs), thus forming larger and more mixed micelles with stronger swelling and dissolution ability, resulting in a relatively high bioaccessibility of betulin. In contrast, the bioaccessibility of betulin in the emulsion prepared by coconut oil (with high saturated fatty acid content) was relatively low (1.17%).ConclusionThe results of this study indicate that selecting an appropriate carrier oil is important for the design of self‐stabilized W/O Pickering emulsions to improve the bioaccessibility of betulin and other lipophilic bioactivities effectively. © 2024 Society of Chemical Industry.
Development of Machine Learning Models for Predicting the 1‐Year Risk of Reoperation After Lower Limb Oncological Resection and Endoprosthetic Reconstruction Based on Data From the PARITY Trial
Authors: Deng Jiawen , Moskalyk Myron , Shammas‐Toma Matthew , Aoude Ahmed , Ghert Michelle , Bhatnagar Sahir , Bozzo Anthony 
Published: September 2024

ABSTRACTBackgroundOncological resection and reconstruction involving the lower extremities commonly lead to reoperations that impact patient outcomes and healthcare resources. This study aimed to develop a machine learning (ML) model to predict this reoperation risk.MethodsThis study was conducted according to TRIPOD + AI. Data from the PARITY trial was used to develop ML models to predict the 1‐year reoperation risk following lower extremity oncological resection and reconstruction. Six ML algorithms were tuned and calibrated based on fivefold cross‐validation. The best‐performing model was identified using classification and calibration metrics.ResultsThe polynomial support vector machine (SVM) model was chosen as the best‐performing model. During internal validation, the SVM exhibited an AUC‐ROC of 0.73 and a Brier score of 0.17. Using an optimal threshold that balances all quadrants of the confusion matrix, the SVM exhibited a sensitivity of 0.45 and a specificity of 0.81. Using a high‐sensitivity threshold, the SVM exhibited a sensitivity of 0.68 and a specificity of 0.68. Total operative time was the most important feature for reoperation risk prediction.ConclusionThe models may facilitate reoperation risk stratification, allowing for better patient counseling and for physicians to implement measures that reduce surgical risks.
Reasons for Surgical Attrition Among Nonmetastatic Upper Gastrointestinal Cancer Patients: A Single Institutional Experience
Authors: Kakish Hanna , Drigotas Claire , Loftus Alexander W. , Boutros Christina S. , Doh Susan J. , Ammori John B. , Rothermel Luke D. , Hoehn Richard S. 
Published: September 2024

ABSTRACTIntroductionUpper gastrointestinal (UGI) cancers require multidisciplinary treatment, but surgery provides the only potentially curative option. We sought to understand reasons for attrition before surgery within our regional hospital network.MethodsWe performed chart reviews of patients (age 18–80) with stage I–III UGI cancers (gastroesophageal junction, gastric, and hepatopancreatobiliary adenocarcinomas) in our multihospital cancer registry from 2015 to 2021. Our primary outcome was reasons for surgical attrition. Univariable analysis identified factors related to surgical attrition and the Kaplan–Meier method estimated overall survival based on surgery receipt.ResultsSeven hundred and ninety‐two patients were included in our analysis, of whom 107 (13.5%) did not undergo curative surgery. Reasons for not undergoing surgery included medical comorbidities (30.8%), patient preference/nonmedical barriers (24.3%, which included: not interested without further explanation, worried about complications, nonadherence to appointments, insurance issues, did not wish for blood transfusion, lack of social support, preferring home care, and worried about recurrence), psychosocial (5.6%), progression while on neoadjuvant therapy or waiting for transplant (15.0% and 7.5%), poor performance status (3.7%), side effects of neoadjuvant therapy (3.7%), and death unrelated to treatment or unknown cause (9.4%). Nonsurgical management was not associated with race, socioeconomic status, or distance traveled for care. Survival was greatly improved for patients who underwent surgery (158 vs. 63 weeks, p < 0.05).ConclusionNearly one in seven patients (18–80 years old) with UGI cancers evaluated at our academic cancer center did not undergo surgical resection. Reasons for surgical attrition included potentially modifiable issues, and addressing these barriers could help overcome inequities in cancer treatment and survival.
Patients With Surgically Resectable Lung Cancer Who Opt for Radiation Have Worse Outcomes
Authors: Song Kimberly J. , Faith Isaac , Tuminello Stephanie , Taioli Emanuela , Rosenzweig Kenneth , Flores Raja M. 
Published: September 2024

ABSTRACTBackgroundSurgery has been the standard procedure for resectable primary LC. Survival after stereotactic body radiation therapy, another treatment, is significantly biased due to preponderance of data from patients deemed unsuitable for surgery. We examined survival of patients refusing surgery in favor of radiation therapy.MethodsWe used the Surveillance, Epidemiology, and End Results database to identify patients with primary Stage I NSCLC diagnosed between 2007 and 2016. Patients were excluded if it was unknown if they were recommended for surgery or if surgery was contraindicated. Multiple predictors were assessed: radiation versus surgery, age at diagnosis, sex, race/ethnicity, health insurance status, marital status, tumor size, and histology. A multivariate analysis was performed to estimate hazard ratios and generate Kaplan−Meier survival curves.ResultsWhen adjusted for confounding variables, survival was greater for patients undergoing surgical resection than those refusing surgery in favor of radiation (HRadj 2.66; 95% CI: 2.27−3.11, p < 0.001) or for those receiving no standardized treatment (HRadj 4.43; 95% CI: 3.57−5.50, p < 0.001).ConclusionsSBRT is an effective treatment for inoperable early LC but there is limited data comparing outcomes against surgical resection. When eligible for both, patients refusing surgery and choosing radiation had worse survival when adjusting for variables including age, tumor size, and histology, and suggests that surgical resection is a superior treatment modality.
Management of Peritoneal Surface Malignancies in Saudi Arabia: An Update
Authors: Helmi Hadeel , Alyami Mohammad , Bin Traiki Thamer , Amin Tarek , Alzahrani Abdulaziz , Alnahawi Mamdouh , Alzahrani Nayef 
Published: September 2024

ABSTRACTPeritoneal surface malignancies (PSM) are aggressive and associated with poor prognosis. Cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (HIPEC) have been used to treat PSM since 1990. In Saudi Arabia, the first HIPEC and pressurized intraperitoneal aerosol chemotherapy (PIPAC) were performed in 2008 and 2019, respectively. With increasing incidences of PSM in Saudi Arabia, the demand for such procedures has grown. This article outlines the status of PSM management in Saudi Arabia and its prospects.
Assessing the Reporting Quality of Machine Learning Algorithms in Head and Neck Oncology
Authors: Alapati Rahul , Renslo Bryan , Wagoner Sarah F. , Karadaghy Omar , Serpedin Aisha , Kim Yeo Eun , Feucht Maria , Wang Naomi , Ramesh Uma , Bon Nieves Antonio , Lawrence Amelia , Virgen Celina , Sawaf Tuleen , Rameau Anaïs , Bur Andrés M. 
Published: September 2024

ObjectiveThis study aimed to assess reporting quality of machine learning (ML) algorithms in the head and neck oncology literature using the TRIPOD‐AI criteria.Data SourcesA comprehensive search was conducted using PubMed, Scopus, Embase, and Cochrane Database of Systematic Reviews, incorporating search terms related to “artificial intelligence,” “machine learning,” “deep learning,” “neural network,” and various head and neck neoplasms.Review MethodsTwo independent reviewers analyzed each published study for adherence to the 65‐point TRIPOD‐AI criteria. Items were classified as “Yes,” “No,” or “NA” for each publication. The proportion of studies satisfying each TRIPOD‐AI criterion was calculated. Additionally, the evidence level for each study was evaluated independently by two reviewers using the Oxford Centre for Evidence‐Based Medicine (OCEBM) Levels of Evidence. Discrepancies were reconciled through discussion until consensus was reached.ResultsThe study highlights the need for improvements in ML algorithm reporting in head and neck oncology. This includes more comprehensive descriptions of datasets, standardization of model performance reporting, and increased sharing of ML models, data, and code with the research community. Adoption of TRIPOD‐AI is necessary for achieving standardized ML research reporting in head and neck oncology.ConclusionCurrent reporting of ML algorithms hinders clinical application, reproducibility, and understanding of the data used for model training. To overcome these limitations and improve patient and clinician trust, ML developers should provide open access to models, code, and source data, fostering iterative progress through community critique, thus enhancing model accuracy and mitigating biases.Level of EvidenceNA Laryngoscope, 135:687–694, 2025
Loss‐of‐function variants in RNA binding motif protein X‐linked induce neuronal defects contributing to amyotrophic lateral sclerosis pathogenesis
Authors: He Di , He Xinyi , Shen Dongchao , Liu Liyang , Yang Xunzhe , Hao Meng , Wang Yi , Li Yi , Liu Qing , Liu Mingsheng , Wang Jiucun , Zhang Xue , Cui Liying 
Published: September 2024

AbstractDespite being one of the most prevalent RNA modifications, the role of N6‐methyladenosine (m6A) in amyotrophic lateral sclerosis (ALS) remains ambiguous. In this investigation, we explore the contribution of genetic defects of m6A‐related genes to ALS pathogenesis. We scrutinized the mutation landscape of m6A genes through a comprehensive analysis of whole‐exome sequencing cohorts, encompassing 508 ALS patients and 1660 population‐matched controls. Our findings reveal a noteworthy enrichment of RNA binding motif protein X‐linked (RBMX) variants among ALS patients, with a significant correlation between pathogenic m6A variants and adverse clinical outcomes. Furthermore, Rbmx knockdown in NSC‐34 cells overexpressing mutant TDP43Q331K results in cell death mediated by an augmented p53 response. Similarly, RBMX knockdown in ALS motor neurons derived from induced pluripotent stem cells (iPSCs) manifests morphological defects and activation of the p53 pathway. Transcriptional analysis using publicly available single‐cell sequencing data from the primary motor cortex indicates that RBMX‐regulated genes selectively influence excitatory neurons and exhibit enrichment in ALS‐implicated pathways. Through integrated analyses, our study underscores the emerging roles played by RBMX in ALS, suggesting a potential nexus between the disease and dysregulated m6A‐mediated mRNA metabolism.
Evaluation of Ischemic Time and Complications in Free Jejunum Transfer
Authors: Suzuki Mayu , Arata Jun , Kaito Shuko 
Published: September 2024

ABSTRACTBackgroundIn free jejunum transfer, knowing the ischemic tolerance time of the jejunum is crucial. It helps determine the need for reharvesting if an unexpected situation prolongs the ischemic time. The current ischemic tolerance time in humans is unknown. We investigated the relationship between ischemic time and postoperative complications in head and neck cancer patients who underwent free jejunum transfer.MethodsThe study included 76 patients with available medical records out of 103 patients who underwent free jejunum transfer between 2009 and 2023. The association between the surgical procedure, including ischemic time, and patient's background, and flap engraftment, stenosis of the intestinal anastomosis, the swallowing function, and other complications was investigated.ResultsThe ischemic time for jejunal flaps ranged from 1 h 24 min to 6 h, with a mean of 197 ± 55.5 min. In 72 patients, the jejunum was successfully engrafted, but vascular occlusion occurred in another four patients. In three of these patients, jejunal necrosis occurred, and there was no specific trend in ischemic time. Stenosis of the intestinal anastomosis occurred in 17 cases (22%), with ischemic time (≥3 h) and age (≥75 years) being significant factors for stenosis (ischemic time: 30% vs. 10%, p = 0.048, age: 50% vs. 15%, p < 0.01). No significant correlations were observed with other complications or the swallowing function.ConclusionThere was no specific trend between ischemic time and jejunal survival rate, indicating that an ischemic time within 6 h may not have affected engraftment. Although we have recently performed intestinal anastomosis prior to vascular anastomosis, the choice of surgical technique should be adapted to the patient's age and background.