bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Validation of an ERCC1 Immunohistochemistry Assay for Solid Tumors
Authors: Bahamon Brittany N. , Gao Feng , Danaee Hadi 
Published: September 2016

Context.—Excision repair cross-complementation 1 (ERCC1) is a key enzyme in nuclear excision repair pathway and has a critical role in helping remove DNA adducts caused by cross-linking agents, such as platinum-containing cancer chemotherapies and other DNA-damaging therapeutic modalities. ERCC1 expression, evaluated by techniques such as immunohistochemistry, has been associated with clinical response; ERCC1+ tumors are more resistant to cisplatin treatment than are ERCC1− tumors. Although several immunohistochemistry, anti-ERCC1 antibodies are available, the 8F1 clone, in particular, has been used in many studies. Recent evidence has suggested that the 8F1 antibody cross-reacts with at least one other protein, raising concerns about the specificity of this clone.Objective.—To design an immunohistochemistry assay to detect ERCC1 levels that show dynamic range and consistent analytic performance.Design.—Two different primary antibodies to ERCC1, clones 4F9 and D6G6, were evaluated on formalin-fixed, paraffin-embedded tissue. We then performed a fit-for-purpose assay validation with the 4F9 clone, which included sensitivity assessment across several solid tumor types and evaluation of analytic parameters, such as precision and reproducibility.Results.—The 4F9 clone was consistently superior to the D6G6 clone in the optimization phase. A range of expression was seen in ovarian, head and neck, non–small cell lung, and esophageal cancer samples when tested with the 4F9 clone. The antibody showed acceptable reproducibility (31.02%) and precision (16.06%).Conclusions.—This assay can be used to assess ERCC1 levels during clinical studies of patient tumors from a variety of tumor types.
Interobserver Agreement of Usual Interstitial Pneumonia Diagnosis Correlated With Patient Outcome
Authors: Hashisako Mikiko , Tanaka Tomonori , Terasaki Yasuhiro , Uekusa Toshimasa , Achcar Rosane D. , Aswad Bassam I. , Bamefleh Hanaa S. , Capelozzi Vera L. , English John C. , Fabro Alexandre T. , Kataoka Kensuke , Hayashi Tomayoshi , Kondoh Yasuhiro , Taniguchi Hiroyuki , Fukuoka Junya 
Published: September 2016

Context.—
The histopathologic criteria for idiopathic pulmonary fibrosis were revised in the American Thoracic Society/European Respiratory Society/Japan Respiratory Society/Latin American Thoracic Association guidelines in 2011. However, the evidence of diagnosis based on the guidelines needs further investigation.

Objective.—
To examine whether the revised histopathologic criteria for idiopathic pulmonary fibrosis improved interobserver agreement among pathologists and the predicted prognosis in patients with interstitial pneumonia.

Design.—
Twenty, consecutive, surgical lung-biopsy specimens from cases of interstitial pneumonia were examined for histologic patterns by 11 pathologists without knowledge of clinical and radiologic data. Diagnosis was based on American Thoracic Society/European Respiratory Society guidelines of 2002 and 2011. Pathologists were grouped by cluster analysis, and interobserver agreement and association to the patient prognosis were compared with the diagnoses for each cluster.

Results.—
The generalized κ coefficient of diagnosis for all pathologists was 0.23. If the diagnoses were divided into 2 groups: usual interstitial pneumonia (UIP)/probable UIP (the UIP group) or possible/not UIP (the non-UIP group), according to the 2011 guidelines, the κ improved to 0.37. The pathologists were subdivided into 2 clusters in which 1 showed an association between UIP group diagnosis and patient prognosis (P &lt; .05).

Conclusions.—
Agreement about pathologic diagnosis of interstitial pneumonia is low; however, results after division into UIP and non-UIP groups provided favorable agreement. The cluster analysis revealed 1 of the 2 clusters providing high interobserver agreement and prediction of patient prognosis.
Do More With Less: Tips and Techniques for Maximizing Small Biopsy and Cytology Specimens for Molecular and Ancillary Testing: The University of Colorado Experience
Authors: Aisner Dara L. , Rumery Mathew D. , Merrick Daniel T. , Kondo Kimi L. , Nijmeh Hala , Linderman Derek J. , Doebele Robert C. , Thomas Natalie , Chesnut Patrick C. , Varella-Garcia Marileila , Franklin Wilbur A. , Camidge D. Ross 
Published: September 2016

Context.—
In an era in which testing of patient tumor material for molecular and other ancillary studies is of increasing clinical importance for selection of therapy, the ability to test on small samplings becomes critical. Often, small samplings are rapidly depleted in the diagnostic workup or are insufficient for multiple ancillary testing approaches.

Objective.—
To describe technical methodologies that can be implemented to preserve and maximize tissue for molecular and other ancillary testing.

Data Sources.—
Retrospective analysis of a case cohort from the University of Colorado, description of techniques used at the University of Colorado, and published literature.

Conclusions.—
Numerous techniques can be deployed to maximize molecular and other ancillary testing, even when specimens are from small samplings. A dedicated process for molecular prioritization has a high success rate, but also increases workload, which must be factored into establishing such a process. Additionally, establishing high-fidelity communication strings is critical for success of dedicated molecular prioritization of samples. Numerous approaches can be deployed for alternative specimen types, and several technical approaches can also aid in maximizing small specimens.
L’évaluation par les pairs en musique contemporaine en France et aux États-Unis
Authors: Fryberger Annelies 
Published: September 2016

Cet article a pour objet l’évaluation par les pairs en musique contemporaine, notamment au sein de deux institutions : le ministère de la Culture (France) et New Music usa (États-Unis). Nous nous arrêtons longuement sur une figure d’évaluateur que nous appelons « l’intermédiaire » (d’après le travail du sociologue Ronald S. Burt), typifiée par ses liens avec plusieurs réseaux de créateurs plutôt que par son ancrage dans un seul réseau cohésif. Cela nous mène à discuter de l’art sonore, un genre qui demande aux créateurs de nourrir des liens avec des réseaux divers, et du succès institutionnel étonnant des compositrices dans ce domaine. S’ensuit une comparaison des différents systèmes de vote utilisés par les deux institutions étudiées, avec une conclusion sur le travail de gatekeeping en musique contemporaine et sur les façons dont ce travail peut influer sur le travail créateur des compositeurs.
Chronic Illness and Quality of Life 5 Years After Displacement Among Rohingya Refugees in Bangladesh
Authors: Hossain Ahmed , Baten Redwan Bin Abdul , Saadi Altaf , Rana Juwel , Rahman Taifur , Reza Hasan Mahmud , Alameddine Mohamad 
Published: September 2024

ImportanceRohingya refugees, forcibly displaced from Myanmar, face challenges adapting to Bangladesh. Examining their quality of life (QOL) is vital to identifying nuanced factors associated with their well-being, informing targeted interventions for an improved QOL.ObjectivesTo identify the QOL among Rohingya refugees 5 years after migration to Bangladesh, with a particular emphasis on understanding the complex interplay between sociodemographic factors and chronic illnesses.Design, Setting, and ParticipantsA cross-sectional study involving resettled Rohingya adults was conducted between May 18 and July 7, 2021, approximately 5 years after their resettlement in Bangladesh. Of the participants, 500 individuals were healthy, whereas 558 individuals were undergoing treatment for at least 1 chronic disease. Data were analyzed from January to February 2024.Main Outcomes and MeasuresThe study assessed QOL using the short version of the World Health Organization’s QOL Questionnaire, covering 4 domains: physical, psychological, social, and environmental. Scores were transformed to a maximum of 100. Tobit linear regression, adjusted for potential confounders, was employed for analysis.ResultsThe study included a total of 1058 respondents, who were predominantly female (630 participants [59.5%]) and had a mean (SD) age of 42.5 (16.1) years. Despite being healthy, individuals without chronic illnesses had median QOL scores ranging from 44 to 56 out of 100, indicating a relatively poor QOL. A total of 260 participants (46.6%) with chronic diseases reported very poor or poor QOL, in contrast to 58 healthy individuals (11.6%) in the fifth year after displacement. Specifically, patients with cancer and those who had multimorbidity exhibited the lowest QOL scores across all domains, with significant reductions in the physical health (10.57 decrease; 95% CI, −12.97 to −8.17) and psychological domain scores (7.20 decrease; 95% CI, −9.71 to −5.93) according to Tobit regression analysis.Conclusions and RelevanceThis study found that chronic illnesses were associated with all domains of QOL among Rohingya refugees, particularly those with musculoskeletal disorders, cancer, and multimorbid conditions. This heightened vulnerability may contribute to poor QOL in this population. By uncovering these disparities, the study lays the groundwork for targeted interventions and policies aligned with the United Nations’ goal of leaving no one behind in sustainable development efforts.
Outcomes by Race and Ethnicity Following a Medicare Bundled Payment Program for Joint Replacement
Authors: Kim Narae , Jacobson Mireille 
Published: September 2024

ImportanceThe Comprehensive Care for Joint Replacement (CJR) model, a traditional Medicare bundled payment program for lower-extremity joint replacement, is associated with care for patients outside traditional Medicare. Whether CJR model outcomes have differed by patient race or ethnicity outside of traditional Medicare is unclear.ObjectiveTo evaluate outcomes associated with the CJR model among Hispanic patients not enrolled in traditional Medicare.Design, Setting, and ParticipantsThis cohort study used hospitalization data from California’s Patient Discharge Dataset for all patients who underwent lower-extremity joint replacement in California between January 1, 2014, and December 31, 2017. In California, 3 metropolitan statistical areas (MSAs) were randomly selected to participate in CJR in April 2016. Hospitals not participating in other Medicare Alternative Payment Models were included in the treated group if they were in these 3 MSAs and in the control group if they were in the remaining 23 MSAs. The data analysis was performed between October 1 and December 31, 2023.ExposureComprehensive Care for Joint Replacement program implementation.Main Outcomes and MeasuresThe main outcomes were hospital length of stay and home discharge rates by race and ethnicity. Home discharge status included self-care, the use of home health services, and hospice care at home. Event study, difference-in-differences, and triple differences models were used to estimate differential changes in health care service use by race and ethnicity for patients in the treated MSAs compared with the control MSAs before vs after CJR implementation.ResultsOf 309 834 hospitalizations (patient mean [SD] age, 68.3 [11.3] years; 60.6% women; 14.8% Hispanic; 72.4% non-Hispanic White), 48.0% were in treated MSAs and 52.0% in control MSAs. The CJR program was associated with an increase in home discharge rates for patients without traditional Medicare coverage; however, the increase differed by patient race and ethnicity. The increase was 0.05 (95% CI, 0.02-0.08) percentage points higher for Hispanic patients with Medicare Advantage and 0.03 (95% CI, 0.01-0.04) percentage points higher for Hispanic patients without Medicare compared with their non-Hispanic White counterparts.Conclusions and RelevanceThis cohort study shows that CJR program outcomes differed by race and ethnicity for patients covered outside traditional Medicare, with home discharge rates increasing more for Hispanic compared with non-Hispanic White patients. These findings suggest the importance of considering differential outcomes of Medicare payment policies for racial and ethnic minority patient populations beyond the initially targeted groups.
New findings on clinical experience on surface‐guided radiotherapy for frameless non‐coplanar stereotactic radiosurgery treatments
Authors: Sánchez‐Rubio Patricia , Rodríguez‐Romero Ruth , Pinto‐Monedero María , Alejo‐Luque Luis , Martínez‐Ortega Jaime 
Published: September 2024

AbstractPurposeThe aim of this study was to assess the accuracy of a surface‐guided radiotherapy (SGRT) system for setup and intra‐fraction motion control in frameless non‐coplanar stereotactic radiosurgery (fSRS) using actual patient data immobilized with two different types of open‐faced masks and employing a novel SGRT systems settings.Methods and materialsForty‐four SRS patients were immobilized with two types of open‐faced masks. Sixty lesions were treated, involving the analysis of 68 cone‐beam scans (CBCT), 157 megavoltage (MV) images, and 521 SGRT monitoring sessions. The average SGRT translations/rotations and 3D vectors (MAG‐Trasl and MAG‐Rot) were compared with CBCT or antero‐posterior MV images for 0° table or non‐coplanar beams, respectively. The intrafraction control was evaluated based on the average shifts obtained from each monitoring session. To assess the association between the SGRT system and the CBCT, the two types of masks and the 3D vectors, a generalized estimating equations (GEE) regression analysis was performed. The Wilcoxon singed‐rank test for paired samples was performed to detect differences in couch rotation with longitudinal (LNG) and lateral (LAT) translations and/or yaw.ResultsThe average SGRT corrections were smaller than those detected by CBCT (≤0.5 mm and 0.1°), with largest differences in LNG and yaw. The GEE analysis indicated that the average MAG‐Trasl, obtained by the SGRT system, was not statistically different (p = 0.09) for both mask types, while, the MAG‐Rot was different (p = 0.01). For non‐coplanar beams, the Wilcoxon singed‐rank test demonstrated no significantly differences for the corrections (LNG, LAT, and yaw) for any table rotation except for LNG corrections at 65° (p = 0.04) and 75° (p = 0.03) table angle position; LAT shifts at 65° (p = 0.03) and 270° (p < 0.001) table angle position, and yaw rotation at 30° (p = 0.02) table angle position. The average intrafraction motion was < 0.1 mm and 0.1° for any table angle.ConclusionThe SGRT system used, along with the novel workflow performed, can achieve the setup and intra‐fraction motion control accuracy required to perform non‐coplanar fSRS treatments. Both masks ensure the accuracy required for fSRS while providing a suitable surface for monitoring.
Identifying dose constraints for the parotid ducts to minimize patient‐reported xerostomia: Is conventional mean dose sparing of the parotid glands sufficient?
Authors: Ahmidouch Manal , Das Shiva K. , Zhu Tong , Shen Colette , Marks Lawrence B. , Chera Bhishamjit S. , Fried David V. 
Published: September 2024

AbstractBackground and purposeThe aim of this study was to identify dose constraints for the parotid ducts that limit patient‐reported xerostomia and estimate whether these constraints are achieved during conventional parotid gland sparing radiation therapy (PGS‐RT).Methods and materialsThirty‐eight oropharyngeal squamous cell carcinoma patients were treated prospectively on trial with MRI sialography‐guided parotid duct sparing radiation therapy (PDS‐RT). PDS‐RT explicitly minimizes dose to the parotid ducts in addition to PGS‐RT. Parotid duct dose constraints were identified that distinguished patients reporting high and low rates of xerostomia. Atlas‐based parotid duct contours were generated on a retrospective cohort of similar patients where the parotid ducts were not contoured nor explicitly spared to estimate the dose received by the parotid ducts during PGS‐RT.ResultsPatients whose intraglandular parotid ducts or total parotid ducts were planned for a mean dose < 14 Gy and < 12 Gy, respectively, reported significantly (p < 0.01) lower rates of xerostomia at 6 and 12 months post‐RT. Patients receiving PDS‐RT had average total and intraglandular duct doses of 11.6 and 13.6 Gy, respectively, compared to an estimated 23.8 and 22.1 Gy, for those receiving PGS‐RT (p < 0.01). Only 6% (6/108) and 20% (22/108) of patients receiving PGS‐RT were estimated to meet the dose constraints for the total ducts and intraglandular ducts, respectively.ConclusionParotid duct dose thresholds exist that appear to distinguish patients with and without xerostomia. The identified dose thresholds are frequently not met in PGS‐RT plans. In addition to reducing the dose to the parotid gland(s), parotid duct sparing may also further reduce xerostomia.
Improving access in medical physics residency programs for physicists with disabilities
Authors: Fagerstrom Jessica M. , Eliason Grace , Al‐Hallaq Hania , Taylor Brian A. , Ashraf Muhammad Ramish , Viscariello Natalie 
Published: September 2024

AbstractWithin the landscape of medical physics education, residency programs are instrumental in imparting hands‐on training and experiential knowledge to early‐career physicists. Ensuring access to educational opportunities for physicists with disabilities is a legal, ethical, and pragmatic requirement for programs, considering that a significant proportion of the United States population has a disability. Grounded in conceptual frameworks of competency‐based medical education and the social model of disability, this work provides an introduction to some practical recommendations for medical physics residency programs. Strategies include embracing universal design principles, fostering partnerships with disability service offices, using inclusive language, developing and publicizing clear procedures for disclosing disabilities and requesting accommodations, and maintaining an overall commitment to equitable access to education. This work urges medical physics residency leadership to proactively move towards training environments that support the needs of residents across the spectrum of disability, highlighting why disability inclusion fundamentally enriches diversity.
Explore the feasibility of using spot‐scanning proton arc therapy for a synchrotron accelerator‐based proton therapy system – A simulation study
Authors: Cong Xiaoda , Liu Gang , Liu Peilin , Zhao Lewei , Chen Shupeng , Li Xiaoqiang , Shen Jiajian , Ding Xuanfeng 
Published: September 2024

AbstractObjectiveThe aim of this study was to evaluate the feasibility and plan quality of spot‐scanning proton arc therapy (SPArc) using a synchrotron‐accelerator‐based proton therapy system compared to intensity‐modulated proton therapy (IMPT).ApproachFive representative disease sites, including head and neck, lung, liver, brain chordoma, and prostate cancers, were retrospectively selected. Both IMPT and SPArc plans are generated with the HITACHI ProBEAT PBS system's minimum MU constraints and physics beam model. The SPArc plans are generated with 2.5° sampling frequency. The static delivery time was simulated based on the previously published synchrotron delivery sequence model, and the dynamic delivery time was simulated using a proton arc gantry mechanical model integrated with the synchrotron delivery sequence. Both dosimetric plan quality and delivery efficiency are evaluated.Main resultsA superior plan quality is reached compared with the IMPT plans generated for the same disease site. However, a relatively prolonged static and dynamic delivery time post new challenge, as static time increased by 49.22% and dynamic time 59.10% on average.SignificanceThis study presents the first simulation results of delivering the SPArc plans using a synchrotron‐accelerated proton therapy system. The result shows its feasibility and limitations, which could guide future development.
Anti Wind‐Up and Robust Data‐Driven Model‐Free Adaptive Control for MIMO Nonlinear Discrete‐Time Systems
Authors: Heydari Mohsen , Novinzadeh Alireza B. , Tayefi Morteza 
Published: September 2024

ABSTRACTThis article addresses a solution to one of the main challenges of online data‐driven control (DDC) methods: reducing the sensitivity of the model‐free adaptive control (MFAC) method to initial conditions and control parameters with the new control cost function and added the output error rate and integral along with a new anti‐wind up strategy for multi‐input multi‐output (MIMO) systems. The parameters introduced to the new control law have been validated using the boundary‐input boundary‐output (BIBO) approach to design and converge the controller. The simulation findings on a nonlinear auto‐regressive moving average model with exogenous inputs (NARMAX) system with triangular control input demonstrate that the proposed control rule will outperform to prototype MFAC. Furthermore, to analyze the sensitivity of the controller to the initial conditions and the uncertainties of the control parameters, 30 Monte Carlo simulations were performed with random initial conditions in the presence of disturbance in the control input, and output noise, and the results were compared with the prototype MFAC and conventional PID controller using standard criteria such as integral time absolute error, standard deviation, steady‐state error, and mean maximum error, which shows a noticeable superiority of proposed controller relative to the prototype MFAC.
Magnetron Sputtering Dual‐Ion Sequential Release Coating on PET Artificial Ligament Promotes Vascular Nerve Regeneration and Graft‐Bone Integration
Authors: Wu Wei , Xia Yuhao , Huang Ye , Wei Wenying , Wu Xiaopei , Tu Rong , Chen Tianwu , Dai Honglian 
Published: September 2024

AbstractAnterior cruciate ligament (ACL) injuries in sports have become increasingly prevalent, leading to the widespread adoption of polyethylene terephthalate (PET) artificial ligaments for ACL reconstruction due to their superior mechanical properties. However, the bio‐inertness of PET presents a significant challenge to graft‐bone integration, necessitating the enhancement of PET surface bioactivity. This study employed magnetron sputtering and hydrogel coating techniques to introduce strontium calcium‐phosphorus, and magnesium ions onto the surface of PET ligaments, achieving the sequential release of Mg, and Sr ions. The scanning electron microscopy analysis confirmed the uniformity and stability of the modified PET ligament surface material. The synergistic effect of sequential release from Mg/Sr‐PET has effectively promoted osteogenesis, angiogenesis, and neuronal differentiation in vitro. Moreover, in the reconstructed ACL model using Sprague‐Dawley rats, the histological staining, micro‐computed tomography, and biomechanical test results indicated that the Mg/Sr‐PET group notably stimulated blood vessel and nerve formation, demonstrating remarkable bone regrowth promotion. In conclusion, the sequential release and synergistic effect of magnesium and strontium ions significantly enhanced graft‐bone integration and accelerated rapid healing, offering valuable insights for improving clinical ACL reconstruction outcomes.