bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incremental retraining, clinical implementation, and acceptance rate of deep learning auto‐segmentation for male pelvis in a multiuser environment
Authors: Duan Jingwei , Vargas Carlos E. , Yu Nathan Y. , Laughlin Brady S. , Toesca Diego Santos , Keole Sameer , Rwigema Jean Claude M. , Wong William W. , Schild Steven E. , Feng Xue , Chen Quan , Rong Yi 
Published: June 2023

AbstractBackgroundDeep learning auto‐segmentation (DLAS) models have been adopted in the clinic; however, they suffer from performance deterioration owing to the clinical practice variability. Some commercial DLAS software provide an incremental retraining function that enables users to train a custom model using their institutional data to account for clinical practice variability.PurposeThis study was performed to evaluate and implement the commercial DLAS software with the incremental retraining function for definitive treatment of patients with prostate cancer in a multi‐user environment.MethodsCT‐based target organs and organs‐at‐risk (OAR) delineation of 215 prostate cancer patients were utilized. The performance of three commercial DLAS software built‐in models was validated with 20 patients. A retrained custom model was developed using 100 patients and evaluated on the remaining data (n = 115). Dice similarity coefficient (DSC), Hausdorff distance (HD), mean surface distance (MSD), and surface DSC (SDSC) were utilized for quantitative evaluation. A multi‐rater qualitative evaluation was blindly performed with a five‐level scale. Visual inspection was performed in consensus and non‐consensus unacceptable cases to identify the failure modes.ResultsThree commercial DLAS vendor built‐in models achieved sub‐optimal performance in 20 patients. The retrained custom model had a mean DSC of 0.82 for prostate, 0.48 for seminal vesicles (SV), and 0.92 for rectum, respectively. This represents a significant improvement over the built‐in model with DSC of 0.73, 0.37, and 0.81 for the corresponding structures. Compared to the acceptance rate of 96.5% and consensus unacceptable rate (i.e., both reviewers rated as unacceptable) of 3.5% achieved by manual contours, the custom model achieved a 91.3% acceptance rate and 8.7% consensus unacceptable rate. The failure modes of retrained custom model were attributed to the following: cystogram (n = 2), hip prosthesis (n = 2), low dose rate brachytherapy seeds (n = 2), air in endorectal balloon(n = 1), non‐iodinated spacer (n = 2), and giant bladder(n = 1).ConclusionThe commercial DLAS software with the incremental retraining function was validated and clinically adopted for prostate patients in a multi‐user environment. AI‐based auto‐delineation of the prostate and OARs is shown to achieve improved physician acceptance, overall clinical utility, and accuracy.
Motion‐corrected model‐based reconstruction for 2D myocardial T1 mapping
Authors: Kerkering Kirsten Miriam , Schulz‐Menger Jeanette , Schaeffter Tobias , Kolbitsch Christoph 
Published: June 2023

PurposeTo allow for T1 mapping of the myocardium within 2.3 s for a 2D slice utilizing cardiac motion‐corrected, model‐based image reconstruction.MethodsGolden radial data acquisition is continuously carried out for 2.3 s after an inversion pulse. In a first step, dynamic images are reconstructed which show both contrast changes due to T1 recovery and anatomical changes due to the heartbeat. An image registration algorithm with a signal model for T1 recovery is applied to estimate non‐rigid cardiac motion. In a second step, estimated motion fields are applied during an iterative model‐based T1 reconstruction. The approach was evaluated in numerical simulations, phantom experiments and in in‐vivo scans in healthy volunteers.ResultsThe accuracy of cardiac motion estimation was shown in numerical simulations with an average motion field error of 0.7 ± 0.6 mm for a motion amplitude of 5.1 mm. The accuracy of T1 estimation was demonstrated in phantom experiments, with no significant difference (p = 0.13) in T1 estimated by the proposed approach compared to an inversion‐recovery reference method. In vivo, the proposed approach yielded 1.3 × 1.3 mm T1 maps with no significant difference (p = 0.77) in T1 and SDs in comparison to a cardiac‐gated approach requiring 16 s scan time (i.e., seven times longer than the proposed approach). Cardiac motion correction improved the precision of T1 maps, shown by a 40% reduced SD.ConclusionWe have presented an approach that provides T1 maps of the myocardium in 2.3 s by utilizing both cardiac motion correction and model‐based T1 reconstruction.
Lung T2* mapping using 3D ultrashort TE with tight intervals δTE
Authors: Malis Vadim , Kassai Yoshimori , Vucevic Diana , Bae Won C. , Ohno Yoshiharu , Yen Andrew , Miyazaki Mitsue 
Published: June 2023

PurposeTo develop 3D ultrashort‐TE (UTE) sequences with tight TE intervals (δTE), allowing for accurate mapping of lungs under free breathing.MethodsWe have implemented a four‐echo UTE sequence with δTE (< 0.5 ms). A Monte‐Carlo simulation was performed to identify an optimal number of echoes that would result in a significant improvement in the accuracy of the fit within an acceptable scan time. A validation study was conducted on a phantom with known short values (< 5 ms). The scanning protocol included a combination of a standard multi‐echo UTE with six echoes (2.2‐ms intervals) and a new four‐echo UTE (TE < 2 ms) with tight TE intervals δTE. The human imaging was performed at 3 T on 6 adult volunteers. mapping was performed with mono‐exponential and bi‐exponential models.ResultsThe simulation for the proposed 10‐echo acquisition predicted over 2‐fold improvement in the accuracy of estimating the short compared with the regular six‐echo acquisition. In the phantom study, the was measured up to three times more accurately compared with standard six‐echo UTE. In human lungs, maps were successfully obtained from 10 echoes, yielding average values  = 1.62 ± 0.48 ms for mono‐exponential and  = 1.00 ± 0.53 ms for bi‐exponential models.ConclusionA UTE sequence using δTE was implemented and validated on short phantoms. The sequence was successfully applied for lung imaging; the bi‐exponential signal model fit for human lung imaging may provide valuable insights into the diseased human lungs.
Material point method‐based simulation of dynamic process of soil landslides considering pore fluid pressure
Authors: Wu Fengyuan , Sun Wei , Li Xinchao , Guan Yongping , Dong Manman 
Published: June 2023

AbstractIn this study, the dynamic process of soil landslides is investigated using the material point method (MPM). A basal friction algorithm is developed based on the MPM, and the pore water pressure is considered for calculating the basal friction. A large‐scale debris flow experiment is performed to validate the effectiveness of the MPM in simulating the dynamic process of soil landslides. The calculated depths of the debris flow using the MPM are consistent with the experimental results. The effects of the basal friction angle and internal friction angle on the debris flow depths are discussed. Moreover, a landslide case is simulated using the MPM, and the calculation results are consistent with the measured results. The horizontal velocity, vertical velocity, velocity direction, and kinetic energy of the landslide are analyzed. Finally, a case involving a different slope near a landslide is evaluated using the MPM. The distributions of velocity in different directions and changes in the average velocity, kinetic energy, and sliding distance are analyzed. By setting a retaining wall, the accumulation height of a landslide accumulated at the retaining wall and the normal force on the retaining wall can be estimated.
A phenotypic approach to obesity treatment
Authors: Zandvakili Inuk , Pulaski Marya , Pickett‐Blakely Octavia 
Published: June 2023

AbstractObesity is a chronic disease that increases morbidity and mortality and adversely affects quality of life. The rapid rise of obesity has outpaced the development and deployment of effective therapeutic interventions, thereby creating a global health crisis. The presentation, complications, and response to obesity treatments vary, yet lifestyle modification, which is the foundational therapeutic intervention for obesity, is often “one size fits all.” The concept of personalized medicine uses genetic and phenotypic information as a guide for disease prevention, diagnosis, and treatment and has been successfully applied in diseases such as cancer, but not in obesity. As we gain insight into the pathophysiologic mechanisms of obesity and its phenotypic expression, specific pathways can be targeted to yield a greater, more sustained therapeutic impact in an individual patient with obesity. A phenotype‐based pharmacologic treatment approach utilizing objective measures to classify patients into predominant obesity mechanism groups resulted in greater weight loss (compared with a non–phenotype‐based approach) in a recent study by Acosta and colleagues. In this review, we discuss the application of lifestyle modifications, behavior therapy and pharmacotherapy using the obesity phenotype–based approach as a framework.
Micronutrient deficiencies in patients with gastrointestinal cancer: To treat or not to treat
Authors: Turkiewicz Joanna , Garcia Michael , Li Zhaoping , Surampudi Vijaya 
Published: June 2023

AbstractNutrition supplements are widely used among patients with cancer. The general public perceives supplements as more natural anticancer and antitoxicity agents, and often supplements are used without the knowledge of the treating physician. In the clinical setting, there are concerns that supplements may decrease effectiveness of chemotherapy and/or radiotherapy and, as a result, supplementation is avoided. There is a body of literature evaluating micronutrient deficiencies, supplementation, and cancer risk; however, little is known about the risks of treatment of micronutrient deficiencies in specific cancers. Of the types of cancers, patients with gastrointestinal cancers are at high risk of developing malnutrition and, subsequently, possible micronutrient deficiencies. This review aims to evaluate the effects of supplementation of specific micronutrients in patients with cancer of the digestive tract.
A mixed three‐field total Lagrangian material point method for phase‐field fracture modeling of nearly incompressible rubber‐like solids
Authors: Zhang Zijian , Hu Zhiqiang , Ye Hongfei , Zhang Hongwu , Zheng Yonggang 
Published: June 2023

AbstractThe rubber‐like solids, as commonly observed materials in nature and engineering areas, often show high extensibility and weak compressibility, which lead to difficulties for modeling the fracture behavior of these materials. In this paper, we propose a mixed three‐field total Lagrangian material point method (TLMPM) to deal with the fracture of nearly incompressible rubber‐like solids. In this method, the phase‐field method combining with perturbed Lagrangian approach is developed to describe the fracture of nearly incompressible materials. Based on the Lagrangian equation, the governing equations of the displacement, pressure and phase fields are derived for the system considering dynamic effect. Then, a mixed three‐field TLMPM discrete formulation with a remapping strategy is then built to solve the problem involving large deformation. Besides, a staggered solving scheme with explicit time integration is developed for the three‐field problem. The accuracy and capabilities of the proposed method for dealing with the fracture of incompressible materials are demonstrated by modeling several quasi‐static and dynamic numerical problems and comparing the results with other numerical methods and experiments. Moreover, the applicability of the method is further proved by an out‐of‐plane tearing case.
Influencing factors of sleep disorders and sleep quality in healthcare workers during the COVID‐19 pandemic: A systematic review and meta‐analysis
Authors: Lv Qian , Zhou Wenguang , Kong Yue , Chen Silu , Xu Baoling , Zhu Fangfang , Shen Xianying , Qiu Zhaojun 
Published: June 2023

AbstractAimThe aim of this study was to identify the influencing factors of sleep disorders and sleep quality in healthcare workers during the COVID‐19 pandemic.DesignSystematic review and meta‐analysis of observational research.MethodsThe databases of the Cochrane Library, Web of Science, PubMed, Embase, SinoMed database, CNKI, Wanfang Data, and VIP were systematically searched. The quality of studies was assessed using the Agency for Healthcare Research and Quality evaluation criteria and the Newcastle–Ottawa scale.ResultsA total of 29 studies were included, of which 20 were cross‐sectional studies, eight were cohort studies, and 1 was a case–control study; 17 influencing factors were finally identified. Greater risk of sleep disturbance was associated with female gender, single relationship status, chronic disease, insomnia history, less exercise, lack of social support, frontline work, days served in frontline work, department of service, night shift, years of work experience, anxiety, depression, stress, received psychological assistance, worried about being infected, and degree of fear with COVID‐19.ConclusionsDuring the COVID‐19 pandemic, healthcare workers did have worse sleep quality than the general population. The influencing factors of sleep disorders and sleep quality in healthcare workers are multifaceted. Identification and timely intervention of resolvable influencing factors are particularly important for preventing sleep disorders and improving sleep.Patient or Public ContributionThis is a meta‐analysis of previously published studies so there was no patient or public contribution.
Prognostic factors of sepsis in children with acute leukemia admitted to the pediatric intensive care unit
Authors: Wu Li , Jin Ming , Wang Ruiqing , Yang Lihua , Lai Xiaorong , Yu Lihua , Lin Danna , Huang Lulu , Zhang Yajie , Zhang Jingxin , Liao Xu , Zi Juan , Yuan Yuting , Zeng Yinghua , Cheng Ming , Tao Shaohua 
Published: June 2023

AbstractObjectiveTo analyze the prognostic factors of sepsis in children with acute leukemia admitted to the pediatric intensive care unit (PICU) and to compare the efficacy of different scoring systems for predicting the outcome of children.MethodsPatients with an acute leukemia diagnosis admitted to a tertiary care university hospital PICU due to sepsis during chemotherapy between May 2015 and August 2022 were retrospectively analyzed through an electronic medical record system.ResultsDuring this period, 693 children with acute leukemia initially diagnosed were admitted to the center, and 155 (22.3%) of them were transferred to PICU due to deterioration of the disease during treatment. Total 109 (70.3%) patients were transferred to PICU due to sepsis. Here, 17 patients was excluded (prior treatment from another hospital; referring from other hospitals; discontinued treatment; incomplete medical record). Of the 92 patients studied, the mortality rate was 35.9%. Multivariate analysis revealed that remission status, lactate level, invasive mechanical ventilation (IMV), and inotropic support within 48 hours after PICU transfer were independent risk factors for PICU mortality. The pediatric sequential organ failure assessment (PSOFA) score had the greatest predictive validity for hospital mortality (area under the receiver operating characteristic curve [AUROC]: 0.83, 95% confidence intervals [CI]: 0.74–0.92), followed by the pediatric early warning score (PEWS) (0.82, 0.73–0.91) and pediatric critical illness score (PCIS) (0.79, 0.69–0.88).ConclusionThe mortality rate among children with acute leukemia complicated with sepsis is high after being transferred to the PICU. Various scoring systems can be used to monitor the clinical status of patients, identify sepsis early, detect critical illness, and determine the optimal time for transfer to the PICU for supportive treatment, thereby improving the prognosis of these patients.
Convergent validity of the Behavior Observation of Students in Schools for elementary school students with disruptive behaviors
Authors: Alperin Alexander , Dudek Christopher M. , Reddy Linda A. , Glover Todd A. , Wiggs Nicole B. , Bronstein Briana 
Published: June 2023

AbstractSystematic direct observations (SDOs) and behavior rating scales are integral to multimethod behavioral assessment approaches. The present study investigated the convergent validity of the Behavior Observation of Students in Schools (BOSS) form, a widely utilized SDO system, with the most frequently used teacher rating scales in schools, the Behavioral Assessment System for Children, Third Edition (BASC‐3) and the Behavioral and Emotional Screening System, third edition (BESS‐3). Specifically, the present study compared independent observer data collection of student on‐task and disruptive behaviors on the BOSS with teachers' ratings of behavioral problems on the BASC‐3 and BESS‐3. Data come from a sample of 136 teachers and 349 students with or at risk of disruptive behavior disorders (DBDs). Pearson correlations were computed between BOSS and teacher ratings on the BASC‐3 and BESS‐3. Findings demonstrated significant, small to moderate correlations. Results indicate evidence of convergent validity for the BOSS and BASC3 assessments and highlight multimethod behavioral assessment's utility in supporting students with or at risk of DBDs.
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography
Authors: Szyrwiel Lukasz , Gille Christoph , Mülleder Michael , Demichev Vadim , Ralser Markus 
Published: June 2023

AbstractIncreased throughput in proteomic experiments can improve accessibility of proteomic platforms, reduce costs, and facilitate new approaches in systems biology and biomedical research. Here we propose combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data‐independent acquisition, and data analysis with the DIA‐NN software suite, to achieve high‐quality proteomic experiments from limited sample amounts, at a throughput of up to 400 samples per day. For instance, when benchmarking our workflow using a 500‐μL/min flow rate and 3‐min chromatographic gradients, we report the quantification of 5211 proteins from 2 μg of a mammalian cell‐line standard at high quantitative accuracy and precision. We further used this platform to analyze blood plasma samples from a cohort of COVID‐19 inpatients, using a 3‐min chromatographic gradient and alternating column regeneration on a dual pump system. The method delivered a comprehensive view of the COVID‐19 plasma proteome, allowing classification of the patients according to disease severity and revealing plasma biomarker candidates.
Plastic bronchitis during childhood: Diversity of presentation, etiology, treatment, and outcomes
Authors: Nayır Büyükşahin Halime , Emiralioglu Nagehan , Sekerel Bulent E. , Soyer Tutku , Oguz Berna , Güzelkaş Ismail , Sunman Birce , Alboğa Didem , Akgül Erdal Meltem , Yalcın Ebru , Doğru Deniz , Ozcelik Ugur , Kiper Nural 
Published: June 2023

AbstractObjectivePlastic bronchitis (PB) is a rare disease in children, and reliable data are scarce. Here, we aimed to analyze the clinical features, management, and outcomes in children with PB.MethodsThe medical data of patients who were followed up with a diagnosis of PB between January 2010 and March 2022 were retrospectively analyzed.ResultsThe median age of 15 patients was 9 (interquartile range: 4–10) years with a male/female ratio of 12/3. Initial symptoms included recurrent pneumonia (33.3%), persistent atelectasis (33.3%), cast expectoration (26.6%), and intense, persistent cough (6.6%). The most common underlying diagnosis was asthma (n = 12, 80%), and six of the patients were newly diagnosed. The most common radiological findings were atelectasis as a consequence of major airway obstruction on chest X‐ray or computed tomography. Five patients, all diagnosed as having asthma, had recurrent PB and required multiple airway procedures for treatment and diagnosis. During a median 7‐year follow‐up of five patients, occasionally cast expectoration was observed in one patient with asthma who had poor compliance with inhaled corticosteroids.ConclusionPB is a common reflection of the different underlying etiologies in the pediatric age group, and treatment and outcomes are closely related to these. It should be kept in mind that asthma can be a predisposing factor for the development of PB.
Template‐guided method for protein–ligand complex structure prediction: Application to CASP15 protein–ligand studies
Authors: Xu Xianjin , Duan Rui , Zou Xiaoqin 
Published: June 2023

AbstractCritical Assessment of Structure Prediction 15 (CASP15) added a new category of ligand prediction to promote the development of protein/RNA‐ligand modeling methods, which have become important tools in modern drug discovery. A total of 22 targets were released, including 18 protein–ligand targets and 4 RNA‐ligand targets. We applied our recently developed template‐guided method to the protein–ligand complex structure predictions. The method combined a physicochemical, molecular docking method, and a bioinformatics‐based ligand similarity method. The Protein Data Bank was scanned for template structures containing the target protein, homologous proteins, or proteins sharing a similar fold with the target protein. The binding modes of the co‐bound ligands in the template structures were used to guide the complex structure prediction for the target. The CASP assessment results show that the overall performance of our method was ranked second when the top predicted model was considered for each target. Here, we analyzed our predictions in detail, and discussed the challenges including protein conformational changes, large and flexible ligands, and multiple diverse ligands in a binding pocket.
Antimicrobial stewardship: Prescribing across the primary care health professions
Authors: Hollingworth Samantha A. , McGuire Treasure , Van Driel Mieke , Begum Nelufa , Ford Pauline J. , Hawley Glenda , Walsh Laurence J. 
Published: June 2023

AbstractWe examined the patterns of antibiotic prescribing by medical and non‐medical prescribers (dentists, nurse practitioners, and midwives) in Australia. We explored trends in the dispensed use of antibiotics (scripts and defined daily dose [DDD] per 1000 population/day) by Australian prescribers over the 12‐year period, 2005–2016. We obtained data on dispensed prescriptions of antibiotics from registered health professionals subsidized on the Pharmaceutical Benefits Scheme (PBS). There were 216.2 million medical and 7.1 million non‐medical dispensed prescriptions for antibiotics over 12 years. The top four antibiotics for medical prescribers were doxycycline; amoxicillin, amoxicillin plus clavulanic acid, and cefalexin, constituting 80% of top 10 use in 2005 and 2016; the top three for non‐medical were amoxicillin, amoxicillin plus clavulanic acid and metronidazole (84% of top 10 use in 2016). The proportional increase in antibiotic use was higher for non‐medical than medical prescribers. While medical prescribers preferentially prescribed broad‐spectrum and non‐medical prescribers moderate‐spectrum antibiotics, there was a large increase in the use of broad‐spectrum antibiotics over time by all prescribers. One in four medical prescriptions were repeats. Overprescribing of broad‐spectrum antibiotics conflicts with national antimicrobial stewardship initiatives and guidelines. The proportional higher increase in antibiotic use by non‐medical prescribers is a concern. To reduce inappropriate use of antibiotics and antimicrobial resistance, educational strategies targeted at all medical and non‐medical prescribers are needed to align prescribing with current best practice within the scope of practice of respective prescribers.