bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-time forecasting within soccer matches through a Bayesian lens
Authors: Divekar Chinmay , Deb Soudeep , Roy Rishideep 
Published: January 2024

Abstract
This article employs a Bayesian methodology to predict the results of soccer matches in real-time. Using sequential data of various events throughout the match, we utilise a multinomial probit regression in a novel framework to estimate the time-varying impact of covariates and to forecast the outcome. English Premier League data from eight seasons are used to evaluate the efficacy of our method. Different evaluation metrics establish that the proposed model outperforms potential competitors inspired by existing statistical or machine learning algorithms. Additionally, we apply robustness checks to demonstrate the model’s accuracy across various scenarios.
Comparison of paired ordinal data with mis-classification and covariates adjustment
Authors: Han Yuanyuan , Lu Zhao-Hua , Li Yimei , Poon Wai-Yin 
Published: January 2024

Abstract
In this paper, we develop an estimation and testing procedure for comparing matched-pair ordinal outcomes in studies with confounding factors. The classification method for the categories of ordinal outcomes that is accessible for all units may be prone to mis-classification, and thus another error-free classification method that can only be affordable for a fraction of the units are used, resulting in a dataset with partial validation. The distribution of categorical variables is modelled using correlated bivariate Gaussian latent variables, and the confounding factors are adjusted as covariates. The mis-classification of ordinal outcomes is addressed by estimating the mis-classification probabilities through the partial validation structure of the dataset. The mis-classification probabilities and the other parameters are estimated by a two-stage maximum likelihood estimator, and the difference between the matched-pair ordinal outcomes are assessed by a Wald test statistic. Simulation studies were conducted to investigate the accuracy of the estimates of the model parameters, and the type I error rates and power of the proposed testing procedure. The motivating dataset from the Garki Project was analysed to demonstrate the applicability of the proposed approach.
Dynamite plots in surgical research over 10 years: a meta-study using machine-learning analysis
Authors: Doggett Thomas J , Way Connor 
Published: January 2024

Abstract

Purpose
Bar charts of numerical data, often known as dynamite plots, are unnecessary and misleading. Their tendency to alter the perception of mean’s position through the within-the-bar bias and their lack of information on the distribution of the data are two of numerous reasons. The machine learning tool, Barzooka, can be used to rapidly screen for different graph types in journal articles.
We aim to determine the proportion of original research articles using dynamite plots to visualize data, and whether there has been a change in their use over time.

Methods
Original research articles in nine surgical fields of research were sampled based on MeSH terms and then harvested using the Python-based biblio-glutton-harvester tool. After harvesting, they were analysed using Barzooka. Over 40 000 original research articles were included in the final analysis. The results were adjusted based on previous validation data with 95% confidence bounds. Kendall τ coefficient with the Mann–Kendall test for significance was used to determine the trend of dynamite plot use over time.

Results
Eight surgical fields of research showed a statistically significant decrease in use of dynamite plots over 10 years. Oral and maxillofacial surgery showed no significant trend in either direction. In 2022, use of dynamite plots, dependent on field and 95% confidence bounds, ranges from ~30% to 70%.

Conclusion
Our results show that the use of dynamite plots in surgical research has decreased over time; however, use remains high. More must be done to understand this phenomenon and educate surgical researchers on data visualization practices.
Gamma irradiation system’s performance tests
Authors: Taubaldiev Azamat , Živanović Miloš 
Published: January 2024

Abstract
This study reviews the performance analysis of a 137Cs irradiation system that has recently been installed in the laboratory of Uzbek National Institute of Metrology. The laboratory is responsible for calibrating calibration facilities and for calibrating most protection level radiation monitoring instruments used in medical, nuclear, industrial and academic settings in Uzbekistan. This system employs the most advanced radiation safety standards, along with 21st century source automation methods. In this work, we review the system’s performance according to ISO 4037 and present measurement uncertainty budget. Our analysis shows excellent results in terms of scattered radiation, beam uniformity and field size, change in source position, test for source impurities, chamber stability and source calibration, and all these parameters fully comply with the requirements of ISO 4037.
Risk factors of diabetes and cancer-specific mortalities in patients with infiltrating ductal carcinoma of the breast: a population-based study
Authors: Elshanbary Alaa Ahmed , Zaazouee Mohamed Sayed , Nourelden Anas Zakarya , Al-Kafarna Mohammed , Matar Sajeda Ghassan , Elsaeidy Ahmed Saad , Ragab Khaled Mohamed , Elhady Mahmoud M. , Albadrani Ghadeer M. , Altyar Ahmed E. , Kensara Osama A. , Abdel-Daim Mohamed M. 
Published: January 2024

Background and aims
Breast cancer is considered one of the most common neoplasms worldwide. Diabetes (DM) increases mortality among postmenopausal patients with breast cancer. Our study aims to identify the risk factors of DM-specific mortality and infiltrating ductal carcinoma (IDC) mortality in patients with IDC of the breast.

Materials and methods
Data of IDC patients were obtained from the Surveillance, Epidemiology, and End Results database from 1975 to 2016. Independent variables included age, race, marital status, the primary site of IDC, breast subtype, the disease stage, grade, chemotherapy, radiation, and surgery. Kaplan–Meier, Cox and Binary regression tests were used to analyze the data using SPSS software.

Results
A total of 673 533 IDC patients were analyzed. Of them, 4224 died due to DM and 116 822 died due to IDC. Factors that increase the risk of overall, IDC-specific, and DM-specific mortalities include older age, black race, widowed, uninsured, regional and distant stages, grade II and III, and no treatment with chemotherapy or radiotherapy or surgery. Additionally, the IDC mortality increased with separated status, all primary sites, all breast subtypes, and stage IV.

Conclusion
In patients with IDC, controlling DM besides cancer is recommended to reduce the mortality risk. Old, black, widowed, uninsured, regional and distant stages, grade II and III, and no treatment are common risk factors for DM- and IDC-mortality.
The blood lactate/serum albumin ratio might represent a good prognostic indicator of 28-day mortality in patients with acute respiratory distress syndrome: a retrospective observational study
Authors: Chen Jiahao , Gao Chang , Yang Ling , Yang Lijuan , He Ying , Guo Shiqi , Sun Yuanxiao , He Siyu , Guo Qiang 
Published: January 2024

Abstract

Background
Acute respiratory distress syndrome (ARDS) is an acute inflammatory lung injury with a high mortality rate. However, previous ARDS prognostic scoring systems or predictors have been limited by complex formulas that are relatively expensive and inconvenient to obtain. Thus, this study aimed to explore the clinical significance of the blood lactate/serum albumin ratio (LAR) in assessing the prognosis of ARDS patients and compare it with other indicators related to 28-day mortality in ARDS patients.

Methods
We conducted a single-center retrospective study involving patients who fulfilled the Berlin definition of ARDS between 2016 and 2021. Clinical data were collected from medical records within 24 hours after ARDS diagnosis. The LAR, neutrophil-to-lymphocyte ratio, and monocyte-to-lymphocyte ratio (MLR) were calculated. The primary clinical outcome was 28-day mortality. The risk factors for 28-day mortality were determined using logistic regression analysis. The receiver operating characteristic curve was used to evaluate the area under the curve (AUC).

Results
A total of 276 ARDS patients met the inclusion criteria and were divided into surviving and nonsurviving groups according to 28-day mortality. There were significant differences in the Acute Physiologic Assessment and Chronic Health Evaluation II scores, Sequential Organ Failure Assessment scores, MLRs, and LARs between the surviving and nonsurviving groups. The AUC for the LAR was 0.790 (P < 0.001), whereas the AUCs for the Acute Physiologic Assessment and Chronic Health Evaluation II score, Sequential Organ Failure Assessment score, neutrophil-to-lymphocyte ratio, and MLR were 0.584, 0.599, 0.524, and 0.587, respectively. After grouping according to an LAR optimal cutoff value of 0.07, 28-day mortality was significantly higher in the high-LAR group than in the low-LAR group (47.18 vs 12.69, P < 0.001).

Conclusions
The LAR is an independent risk factor for 28-day mortality in ARDS patients and can be used to assess the severity of ARDS to a certain extent, making it superior to other commonly used indicators.
Golden Ratio Flap Designed Using the Golden Ratio Rectangle
Authors: Sakamoto Akio , Fujita Toshiharu , Noguchi Takashi , Matsuda Shuichi 
Published: January 2024

Background:
Rotation flaps are arcuate repairs that redistribute tension vectors and recruit adjacent and/or distant tissue laxity. The incision curve could be a logarithmic spiral curve to reduce the length of an incision. We propose a rotation flap—the golden ratio flap—designed using a golden rectangle.

Methods:
The flap incision is an arc though the major square which is beside the minor square of a golden rectangle. The defect is attached to the line of another minor square and diagonal to the major square. The bottom line runs from the incision end to the tangent point of the circle or the oval, and the perpendicular height line runs from the bottom line to the cross point of the flap incision. These parameters were analyzed retrospectively for four superficial sarcomas that were treated using a rotation flap with an incision approximating the logarithmic spiral curve.

Results:
The ratio of height to bottom of the golden ratio flap design was highly similar to the preoperative flap design in the four cases assessed. With the new design, the ratio of bottom to the defect diameter (minor axis in the oval defect) was 1.3, and for the height, it was 1.4.

Conclusions:
The golden ratio flap, designed using the golden rectangle, is reproducible. The parameters of height and bottom approximate the flap shape, or the length and width, respectively. For clinical applications, step-by-step guidance for drawing the new flap are also proposed.
Accuracy of Cancer Registry Primary Payer Information and Implications for Policy Research
Authors: Davidoff Amy J. , Enewold Lindsey , Williams Courtney P. , Bhattacharya Manami , Sanchez Janeth I. 
Published: January 2024

Background:
Cancer registry-based “primary payer at diagnosis” (PPDx) data are commonly used to evaluate the effect of insurance on cancer care outcomes, yet little is known about how well they capture Medicaid or Medicare enrollment.

Methods:
We linked the National Cancer Institute’s Surveillance, Epidemiology, and End Results registry data to monthly Centers for Medicare and Medicaid Services (CMS) Medicaid and Medicare enrollment records, state-year Medicaid policy, and managed care enrollment. We selected adults aged 19–64 years diagnosed between 2007 and 2011. We used bivariate analyses to compare PPDx to CMS enrollment at diagnosis month and assessed underreporting rates by patient characteristics and state-year policy.

Results:
PPDx reported 7.8% Medicare and 10.1% Medicaid, whereas CMS enrollment indicated 5.5% Medicare, 10.4% Medicaid, and 3.4% dual Medicare-Medicaid (N = 896,031). Positive predictive values for PPDx assignment to Medicaid and Medicare were 65.3% and 75.4%, with false negative rates of 52.0% and 33.8%, respectively. Medicaid underreporting was higher in low (56.5%) versus high (50.8%) poverty areas, for males (56.1%) versus females (48.9%), for Medicaid poverty expansion or waiver enrolled (63.8%) versus cash assistance-related eligibility (47.3%), and in states with large managed care enrollment (all P < 0.001). If Medicaid and Medicare enrollment data were used to edit PPDx, 12.0% of persons would switch primary payer assignment.

Conclusions:
Registry-reported PPDx fails to fully capture Medicaid and Medicare enrollment, which may result in biased estimates of insurance-related policy impacts. Enhancement with objective enrollment data could reduce measurement error and bias in estimates necessary to support policy assessment.
Integrins in biliary injury and fibrosis
Authors: Schaub Johanna R. , Chen Jennifer Y. , Turner Scott M. 
Published: January 2024

Purpose of review
Current treatment options for cholangiopathies are severely limited and there is thus a critical need to identify and develop therapies. This review discusses the role of integrins in biliary injury and fibrosis and their potential as therapeutic targets.

Recent findings
There are a diverse set of roles that integrins play in biliary injury and fibrosis. Some integrins activate TGF-β signaling or are involved in sensing of the extracellular matrix, making them attractive targets for biliary fibrosis. In recent work, autoantibodies to αvβ6 were identified in patients with PSC, supporting the relevance of this integrin in the disease. In addition, a role for α2β1 in cyst formation was identified in a mouse model of polycystic liver disease. Leukocyte integrins (e.g. αEβ7 and α4β7) contribute to lymphocyte trafficking, making them potential targets for biliary inflammation; however, this has not yet translated to the clinic.

Summary
While all members of the same family of proteins, integrins have diverse roles in the pathogenesis of biliary disease. Targeting one or multiple of these integrins may slow or halt the progression of biliary injury and fibrosis by simultaneously impacting different pathologic cells and processes.
Targeting osteopontin to treat primary sclerosing cholangitis
Authors: De Muynck Kevin , Devisscher Lindsey 
Published: January 2024

Purpose of review
Primary sclerosing cholangitis is a chronic cholestatic liver disease for which no pharmacological treatment options are available. It is an immune-mediated disease and macrophages have been implicated in disease pathogenesis. However, which specific macrophage populations contribute to disease, and how we can apply this as therapeutic strategy is still unclear.

Recent findings
Recent studies have shown that fibrous tissue is characterized by osteopontin-positive macrophages, including in patients with primary sclerosing cholangitis. Experimental models indicate that intracellular osteopontin in macrophages confers protection, while secreted osteopontin contributes to disease. Serum osteopontin is increased in different liver diseases, including primary sclerosing cholangitis, and might thus serve as therapeutic target.

Summary
Although several studies report on the role of osteopontin in liver disease, only a minority of the studies have focused on isoform-specific functions, and the importance of the cellular source of secreted osteopontin. Future studies investigating these aspects, and how this can be translated to therapies for primary sclerosing cholangitis, and other chronic liver diseases, are required.
Vascular Neoplasms With NFATC1/C2 Gene Alterations
Authors: Dashti Nooshin K. , Perret Raul , Balzer Bonnie , Naous Rana , Michal Michael , Dermawan Josephine K. , Antonescu Cristina R. 
Published: January 2024

Despite significant advances in their molecular pathogenesis, skeletal vascular tumors remain diagnostically challenging due to their aggressive radiologic appearance and significant morphologic overlap. Within the epithelioid category and at the benign end of the spectrum, recurrent FOS/FOSB fusions have defined most epithelioid hemangiomas, distinguishing them from epithelioid hemangioendothelioma and angiosarcoma. More recently, the presence of EWSR1/FUS::NFATC1/2 fusions emerged as the genetic hallmark of a novel group of unusual vascular proliferations, often displaying epithelioid morphology, with alternating vasoformative and solid growth, variable atypia, reminiscent of composite hemangioendothelioma. In this study, we further our understanding and morphologic spectrum of NFATC-fusion positive vascular neoplasms by describing 9 new cases, including soft tissue locations and novel fusion partners. Combining with the initial cohort of 5 cases, a total of 14 patients were analyzed, showing slight female predilection and an age range of 10 to 66 (mean 42 y). Twelve patients had solitary lesions, while 2 had multifocal polyostotic (pelvic bones) disease. Overall, 12 lesions were intra-osseous and 2 in soft tissue. By targeted RNA Fusion panels or FISH, there were 6 cases of EWSR1::NFATC1, 4 EWSR1::NFATC2, 2 FUS::NFATC2, 1 EWSR1 rearrangement, and 1 with a novel FABP4::NFATC2 fusion. Follow-up was available in 4 patients. One patient experienced 2 local recurrences, 11 and 15 years postdiagnosis, and one patient experienced progressive disease despite multimodality treatment (curettings, embolization, radiation) over 3 years. In summary, our extended investigation confirms that NFATC-related fusions define a distinct group of vascular neoplasms with variable architecture, epithelioid phenotype, and cytologic atypia, commonly located in the bone, occasionally multifocal and with potential for local recurrence and aggressive behavior but no metastatic potential. Molecular analysis is recommended in diagnostically challenging cases with atypical histology to exclude malignancy.
Persistent Risk of Developing Autoimmune Diseases Associated With COVID-19
Authors: Inokuchi Shoichiro , Shimamoto Koji 
Published: January 2024

Objective
This study aimed to investigate the risk of developing autoimmune diseases associated with coronavirus disease 2019 (COVID-19) in Japan, including long-term risks and risks specific to different variants of concern.

Methods
This observational study used an electronic medical record database in Japan. The COVID-19 group is composed of patients diagnosed with COVID-19, whereas the non–COVID-19 group had data sampled from the database. The outcomes of interest encompassed several autoimmune diseases, including rheumatoid arthritis, systemic sclerosis, and immunoglobulin G4–related disease, as well as a composite of these diseases (any autoimmune disease). We examined the relative risk of autoimmune diseases using standardized mortality ratio weighting and the Cox proportional hazards model. Subgroup analyses based on epidemic variants were performed. In addition, short- and long-term risks were investigated using piecewise constant hazard models.

Results
A total of 90,855 COVID-19 and 459,827 non–COVID-19 patients were included between January 16, 2020, and December 31, 2022. The relative risk of any autoimmune disease was 2.32 (95% confidence interval, 2.08–2.60). All the investigated outcomes showed a significant risk associated with COVID-19. Several autoimmune diseases exhibit a risk associated with COVID-19 in the short to long term, and the long-term risk is substantial for systemic sclerosis and immunoglobulin G4–related disease. The variant-specific risk varied across outcomes.

Conclusions
COVID-19 is associated with an increased risk of developing autoimmune diseases in the Japanese population, and this effect persists for a long time. This study provides insights into the association between viral infections and autoimmunity.
Exploring the Clinical Use of Molecular Profiling of Intrahepatic Cholangiocarcinoma in a Comprehensive Multidisciplinary Clinic
Authors: Purchla Julia , Ghabi Elie M , Burns William R , Lafaro Kelly J , Burkhart Richard A , Cameron John L , Yarchoan Mark , Shubert Christopher R , Baretti Marina , He Jin 
Published: January 2024

BACKGROUND:
Molecular profiling of intrahepatic cholangiocarcinoma (ICC) can detect actionable molecular alterations and guide targeted therapies. We explore the clinical use of molecular profiling of ICC in our comprehensive multidisciplinary clinic.

STUDY DESIGN:
Patients with a tissue diagnosis of ICC seen between 2019 and 2023 were identified. A retrospective review was performed to identify their molecular profiles and targeted therapy. The association between the detection of actionable molecular alterations and overall survival (OS) from the first clinic visit date was studied. Patients with an OS of less than 2 months were excluded.

RESULTS:
Among 194 patients with ICC, 125 had molecular profiling. Actionable molecular alterations were detected in 56 (45%) patients, including microsatellite instability (n = 3), high tumor mutational burden (>10 muts/mb; n = 5), isocitrate dehydrogenase 1 and 2 mutations (n = 22 and 6, respectively), BRAF V600E mutations (n = 2), phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha mutations (n = 7), breast cancer 1 and breast cancer 2 mutations (n = 5), mesenchymal epithelial transition amplification (n = 2), fibroblast growth factor receptor 2 and 3 fusions (n = 13), erb-b2 receptor tyrosine kinase 2 overexpression (n = 6), and receptor tyrosine kinase 1 fusion (n = 1). Twenty-one patients received targeted therapies during their treatment course. Survival analysis revealed that for 120 patients with molecular profiling, the detection of an actionable molecular alteration was associated with improved mean OS (34.1 vs 23.6 months, p = 0.008). Among 70 patients with nonmetastatic ICC, the detection of an actionable molecular alteration was associated with improved mean OS (32.1 vs 27.5 months, p = 0.02).

CONCLUSIONS:
Actionable molecular alterations were frequently observed in patients with ICC. Detection of actionable alterations was associated with improved OS. The role of targeted therapy needs further exploration in prospective multicenter studies.
Evolutionary relationships between metabolism and behaviour require genetic correlations
Authors: Crespel Amélie , Lindström Jan , Elmer Kathryn R. , Killen Shaun S. 
Published: January 2024

As selection acts on multivariate phenotypes, the evolution of traits within populations not only depends on the genetic basis of each trait, but also on the genetic relationships among traits. As metabolic rate is often related to vital traits such as growth, physiology and behaviour, its variation and evolution is expected to have important repercussions on individual fitness. However, the majority of the correlations between metabolic rate and other traits has been based on phenotypic correlations, while genetic correlations, basis for indirect selection and evolution, have been overlooked. Using a case study, we explore the importance of properly estimating genetic correlations to understand and predict evolution of multivariate phenotypes. We show that selection on metabolic traits could result in indirect selection mainly on growth-related traits, owing to strong genetic correlations, but not on swimming or risk-taking and sociability behaviour even if they covary phenotypically. While phenotypic correlation can inform about genetic correlation direction, caution is needed in predicting the magnitude of genetic correlation. Therefore, even though phenotypic correlations among physiological and behavioural traits could be useful, deriving evolutionary conclusions based purely on them is not robust. In short, proper estimation of genetic correlations is needed when predicting evolutionary consequences.
This article is part of the theme issue ‘The evolutionary significance of variation in metabolic rates’.