bluuebunny/crossref_metadata_2025_split huggingface dataset:
Update of penetrance estimates in Birt-Hogg-Dubé syndrome
Authors: Bruinsma Fiona Jane , Dowty James G , Win Aung Ko , Goddard Laura C , Agrawal Prachi , Attina' Domenico , Bissada Nabil , De Luise Monica , Eisen Daniel B , Furuya Mitsuko , Gasparre Giuseppe , Genuardi Maurizio , Gerdes Anne-Marie , Hansen Thomas Van Overeem , Houweling Arjan C , Johannesma Paul Christiaan , Lencastre André , Lim Derek , Lindor Noralane M , Luzzi Valentina , Lynch Maeve , Maffé Antonella , Menko Fred H , Michels Guido , Pulido Jose S , Ryu Jay H , Sattler Elke C , Steinlein Ortrud K , Tomassetti Sara , Tucker Kathy , Turchetti Daniela , van de Beek Irma , van Riel Lore , van Steensel Maurice , Zenone Thierry , Zompatori Maurizo , Walsh Jennifer , Bondavalli Davide , Maher Eamonn R , Winship Ingrid M ,   Genetic Susceptibility Working Group I-CONFIRM
Published: February 2023

BackgroundBirt-Hogg-Dubé (BHD) syndrome is a rare genetic syndrome caused by pathogenic or likely pathogenic germline variants in theFLCNgene. Patients with BHD syndrome have an increased risk of fibrofolliculomas, pulmonary cysts, pneumothorax and renal cell carcinoma. There is debate regarding whether colonic polyps should be added to the criteria. Previous risk estimates have mostly been based on small clinical case series.MethodsA comprehensive review was conducted to identify studies that had recruited families carrying pathogenic or likely pathogenic variants inFLCN. Pedigree data were requested from these studies and pooled. Segregation analysis was used to estimate the cumulative risk of each manifestation for carriers ofFLCNpathogenic variants.ResultsOur final dataset contained 204 families that were informative for at least one manifestation of BHD (67 families informative for skin manifestations, 63 for lung, 88 for renal carcinoma and 29 for polyps). By age 70 years, male carriers of theFLCNvariant have an estimated 19% (95% CI 12% to 31%) risk of renal tumours, 87% (95% CI 80% to 92%) of lung involvement and 87% (95% CI 78% to 93%) of skin lesions, while female carriers had an estimated 21% (95% CI 13% to 32%) risk of renal tumours, 82% (95% CI 73% to 88%) of lung involvement and 78% (95% CI 67% to 85%) of skin lesions. The cumulative risk of colonic polyps by age 70 years old was 21% (95% CI 8% to 45%) for male carriers and 32% (95% CI 16% to 53%) for female carriers.ConclusionsThese updated penetrance estimates, based on a large number of families, are important for the genetic counselling and clinical management of BHD syndrome.
Heated tobacco products do not help smokers quit or prevent relapse: a longitudinal study in Japan
Authors: Odani Satomi , Tsuno Kanami , Agaku Israel T , Tabuchi Takahiro 
Published: February 2023

Background
Heated tobacco products (HTPs) are often marketed as a safer alternative to help cigarette smokers quit. We investigated the link between HTP use and smoking cessation and relapse.

Methods
7044 adults (≥20 years old) with at least two observations over three waves (2019–2021) of a longitudinal, nationwide, internet-based survey were classified into current (past 30-day), former and never cigarette smokers. ≥1 month and ≥6 months smoking cessation and smoking relapse at 1-year follow-up were assessed in relation to current HTP use at baseline. Generalised estimating equation models were weighted to account for population differences between HTP users and non-users. Adjusted prevalence ratios (APRs) were computed within population subgroups.

Results
At baseline, 17.2%, 9.1% and 6.1% of the respondents were current cigarette smokers, HTP users and dual users, respectively. Among current established smokers (having smoked regularly, n=1910), HTP use was significantly associated with a decreased likelihood of ≥1 month cessation within those who reported having used evidence-based cessation measures (APR=0.61), smoking 20+ cigarettes per day (APR=0.62), high school education or less (APR=0.73) and fair/poor health (APR=0.59). Negative associations were also seen for ≥6 months cessation among those aged 20–29 years (APR=0.56) and full-time workers (APR=0.56). Among former smokers (n=2906), HTP use was associated with smoking relapse within those who last smoked >1 year ago (APR=1.54), among women (APR=1.61), those aged 20–29 years (APR=2.09), those reporting high school education or less (APR=2.36), those who were unemployed/retired (AOR=3.31) and never/non-current alcohol users (APR=2.10).

Conclusion
HTP use did not help smokers quit or prevent former smokers from relapsing. HTPs should not be recommended as a cessation aid.
Enhancer Coamplification and Hijacking Promote Oncogene Expression in Liposarcoma
Authors: Liu Tingting , Wang Juan , Yang Hongbo , Jin Qiushi , Wang Xiaotao , Fu Yihao , Luan Yu , Wang Qixuan , Youngblood Mark W. , Lu Xinyan , Casadei Lucia , Pollock Raphael , Yue Feng 
Published: February 2023

AbstractLiposarcoma (LPS) is the most common soft-tissue sarcoma in adults with two major subtypes, well differentiated and dedifferentiated. Both subtypes are characterized with the pathognomonic giant ring or marker chromosomes that harbor high copy numbers of known oncogenes. Here, we reported a comprehensive molecular characterization of both tumor and normal tissues from the same patients with LPS, including whole-genome sequencing (WGS), transcriptome, enhancer landscape, and genome-wide three-dimensional (3D) genome structure by Hi-C. Tumor-specific transcripts and regulatory elements were identified, and enhancer coamplification and hijacking events were discovered as novel mechanisms upregulating oncogenes such as MDM2, CDK4, and HMGA2. Combining Hi-C, optical mapping, nanopore long reads, and WGS data partially resolved complex structural variations and reconstructed the local genome and the giant chromosome. Overall, this study provides a comprehensive resource for LPS research and offers insights into how altered enhancers and the 3D genome contribute to gene dysregulation in cancer.Significance:Comprehensive profiling of the enhancer landscape and 3D genome structure in liposarcoma identifies extensive enhancer-oncogene coamplification and enhancer hijacking events, deepening the understanding of how oncogenes are regulated in cancer.
Polyunsaturated Fatty Acid–Bound α-Fetoprotein Promotes Immune Suppression by Altering Human Dendritic Cell Metabolism
Authors: Munson Paul V. , Adamik Juraj , Hartmann Felix J. , Favaro Patricia M.B. , Ho Daniel , Bendall Sean C. , Combes Alexis J. , Krummel Matthew F. , Zhang Karen , Kelley Robin K. , Butterfield Lisa H. 
Published: February 2023

Abstract

α-Fetoprotein (AFP) is expressed by stem-like and poor outcome hepatocellular cancer tumors and is a clinical tumor biomarker. AFP has been demonstrated to inhibit dendritic cell (DC) differentiation and maturation and to block oxidative phosphorylation. To identify the critical metabolic pathways leading to human DC functional suppression, here, we used two recently described single-cell profiling methods, scMEP (single-cell metabolic profiling) and SCENITH (single-cell energetic metabolism by profiling translation inhibition). Glycolytic capacity and glucose dependence of DCs were significantly increased by tumor-derived, but not normal cord blood–derived, AFP, leading to increased glucose uptake and lactate secretion. Key molecules in the electron transport chain in particular were regulated by tumor-derived AFP. These metabolic changes occurred at mRNA and protein levels, with negative impact on DC stimulatory capacity. Tumor-derived AFP bound significantly more polyunsaturated fatty acids (PUFA) than cord blood–derived AFP. PUFAs bound to AFP increased metabolic skewing and promoted DC functional suppression. PUFAs inhibited DC differentiation in vitro, and ω-6 PUFAs conferred potent immunoregulation when bound to tumor-derived AFP. Together, these findings provide mechanistic insights into how AFP antagonizes the innate immune response to limit antitumor immunity.

Significance:
α-Fetoprotein (AFP) is a secreted tumor protein and biomarker with impact on immunity. Fatty acid–bound AFP promotes immune suppression by skewing human dendritic cell metabolism toward glycolysis and reduced immune stimulation.
Precipitation Estimation Based on Infrared Data with a Spherical Convolutional Neural Network
Authors: Yi Lu , Gao Zhangyang , Shen Zhehui , Lin Haitao , Liu Zicheng , Ma Siqi , Wang Cunguang , Li Stan Z. , Li Ling 
Published: February 2023

Abstract
Precipitation is a vital process in the water cycle. Accurate estimation of the precipitation rate underpins the success of hydrological simulations, flood predictions, and water resource management. Satellite infrared (IR) data, with high temporal resolution and wide coverages, have been commonly used in precipitation inversion. However, existing IR-based precipitation retrieval algorithms suffer from various problems such as overestimation in dry regions, poor performance in extreme rainfall events, and reliance on an empirical cloud-top brightness–rain rate relationship. To resolve these problems, we construct a deep learning model using a spherical convolutional neural network to properly represent Earth’s spherical surface. With data input directly from IR bands 3, 4, and 6 of the operational Geostationary Operational Environmental Satellite (GOES), our new model of Precipitation Estimation based on IR data with Spherical Convolutional Neural Network (PEISCNN) was first trained and tested with a 3-month-long dataset, and then validated in a 2-yr period. Compared to the commonly used IR-based precipitation product PERSIANN-CCS (Precipitation Estimation from Remotely Sensed Information Using Artificial Neural Networks–Cloud Classification System), PEISCNN showed significant improvement in the metrics of POD, CSI, RMSE, and CC, especially in the dry region and for extreme rainfall events. Decomposed with the four-component error decomposition (4CED) method, the overestimation of PEISCNN was averaged 47.66% lower than the CCS at the hourly scale. The PEISCNN model may provide a promising way to produce an improved IR-based precipitation product to benefit a wide range of hydrological applications.

Significance Statement
An IR-based precipitation algorithm is irreplaceable in satellite precipitation inversion, since an IR sensor can provide observations of high frequency, fine temporal resolution, and wide coverage. Considering the spherical nature of Earth’s surface which has been overlooked in previous IR-based precipitation retrieval algorithms, we proposed a new deep learning model PEISCNN, which can address the problems that exist in IR-based precipitation estimations such as overestimation in dry regions, deficiency in extreme rainfall events, and reliance on the empirical cloud-top brightness–rain rate relationship. PEISCNN provides a new insight to improve the accuracy of the satellite IR-based or multisensor-based precipitation estimation, and it has great potential to benefit a range of related hydrological research, applications in water resource management, and flood predictions.
Neoliberal Resource Nationalism: The Scramble for Mexico’s Hydrocarbons
Authors: Wattnem Tamara A. 
Published: February 2023

PEMEX, Mexico’s state oil company, was fiercely defended against privatization proposals throughout most of Mexico’s neoliberalization process, even as hundreds of state-owned enterprises were privatized, for two major reasons. First, the state increasingly came to depend on oil income to guarantee its fiscal needs, and this allowed it to postpone a tax reform, to the benefit of economic elites. Second, the meaning of oil in Mexican political culture partially shielded the energy sector from privatization attempts. Paying attention to the state’s fiscal interests, resource nationalism, domestic elite interests, and the meaning with which economic sectors are imbued adds explanatory leverage to our understanding of neoliberalism’s variegated implementation. Aun cuando cientos de empresas estatales fueron privatizadas, PEMEX, la compañía petrolera estatal de México, contó con una feroz defensa frente a las propuestas de privatización durante la mayor parte del proceso de neoliberalización mexicano. Esto obedeció a dos razones principales. La primera es que el Estado llegó a depender cada vez más de los ingresos petroleros para garantizar sus necesidades fiscales, asunto que le permitió posponer una reforma fiscal en beneficio de las élites económicas. La segunda es que el significado del petróleo en la cultura política mexicana protegió parcialmente al sector energético de los intentos de privatización. Si prestamos atención a los intereses fiscales del Estado, el discurso nacionalista en torno a los recursos, los intereses de las élites nacionales y el significado con el que están imbuidos los sectores económicos tendremos un entendimiento más completo de la variada implementación del neoliberalismo.
Optimal Epidemic Control under Uncertainty: Tradeoffs between Information Collection and Other Actions
Authors: Flaig Julien , Houy Nicolas 
Published: February 2023

Background Recent epidemics and measures taken to control them—through vaccination or other actions—have highlighted the role and importance of uncertainty in public health. There is generally a tradeoff between information collection and other uses of resources. Whether this tradeoff is solved explicitly or implicitly, the concept of value of information is central to inform policy makers in an uncertain environment. Method We use a deterministic SIR (susceptible, infectious, recovered) disease emergence and transmission model with vaccination that can be administered as 1 or 2 doses. The disease parameters and vaccine characteristics are uncertain. We study the tradeoffs between information acquisition and 2 other measures: bringing vaccination forward and acquiring more vaccine doses. To do this, we quantify the expected value of perfect information (EVPI) under different constraints faced by public health authorities (i.e., the time of the vaccination campaign implementation and the number of vaccine doses available). Results We discuss the appropriateness of different responses under uncertainty. We show that, in some cases, vaccinating later or with less vaccine doses but more information about the epidemic, and the efficacy of control strategies may bring better results than vaccinating earlier or with more doses and less information, respectively. Conclusion In the present methodological article, we show in an abstract setting how clearly defining and treating the tradeoff between information acquisition and the relaxation of constraints can improve public health decision making. Highlights Uncertainties can seriously hinder epidemic control, but resolving them is costly. Thus, there are tradeoffs between information collection and alternative uses of resources. We use a generic SIR model with vaccination and a value-of-information framework to explore these tradeoffs. We show in which cases vaccinating later with more information about the epidemic and the efficacy of control measures may be better—or not—than vaccinating earlier with less information. We show in which cases vaccinating with fewer vaccine doses and more information about the epidemic and the efficacy of control measures may be better—or not—than vaccinating with more doses and less information.
Performance of machine learning-based coronary computed tomography angiography for selecting revascularization candidates
Authors: Huang Zengfa , Ding Yi , Yang Yang , Zhao Shengchao , Zhang Shutong , Xiao Jianwei , Ding Chengyu , Guo Ning , Li Zuoqin , Zhou Shiguang , Cao Guijuan , Wang Xiang 
Published: February 2023

Background Limited studies have investigated the accuracy of therapeutic decision-making using machine learning-based coronary computed tomography angiography (ML-CCTA) compared with CCTA. Purpose To investigate the performance of ML-CCTA for therapeutic decision compared with CCTA. Material and Methods The study population consisted of 322 consecutive patients with stable coronary artery disease. The SYNTAX score was calculated with an online calculator based on ML-CCTA results. Therapeutic decision-making was determined by ML-CCTA results and the ML-CCTA-based SYNTAX score. The therapeutic strategy and the appropriate revascularization procedure were selected using ML-CCTA, CCTA, and invasive coronary angiography (ICA) independently. Results The sensitivity, specificity, positive predictive value, negative predictive value, accuracy of ML-CCTA and CCTA for selecting revascularization candidates were 87.01%, 96.43%, 95.71%, 89.01%, 91.93%, and 85.71%, 87.50%, 86.27%, 86.98%, 86.65%, respectively, using ICA as the standard reference. The area under the receiver operating characteristic curve (AUC) of ML-CCTA for selecting revascularization candidates was significantly higher than CCTA (0.917 vs. 0.866, P = 0.016). Subgroup analysis showed the AUC of ML-CCTA for selecting percutaneous coronary intervention (PCI) or coronary artery bypass graft (CABG) candidates was significantly higher than CCTA (0.883 vs. 0.777, P < 0.001, 0.912 vs. 0.826, P = 0.003, respectively). Conclusion ML-CCTA could distinguish between patients who need revascularization and those who do not. In addition, ML-CCTA showed a slightly superior to CCTA in making an appropriate decision for patients and selecting a suitable revascularization strategy.
Clinical observation of glucocorticoid therapy for critically ill patients with COVID-19 pneumonia
Authors: Zhu Yingjie , Chen Dongmei , Zhu Yanfang , Ge Xuhua , Li Zhuo , Miao Hongjun 
Published: February 2023

Objective We aimed to investigate the clinical effects of intravenous glucocorticoid (GC) therapy for severe COVID-19 pneumonia. Methods Seventy-two patients hospitalized with severe COVID-19 pneumonia who were discharged or died between 5 January 2020 and 3 March 2020 at Huangshi Infectious Disease Hospital were included. Patients were divided into a treatment group (GC group) and non-treatment group (non-GC group) according to whether they had received GCs within 7 days of hospital admission. Results There was no significant difference between groups for Acute Physiology and Chronic Health Evaluation (APACHE) II score and 28-day survival rate. The rate of invasive mechanical ventilation was higher in the GC group than in the non-GC group. On day 7 after admission, the GC group had shorter fever duration and higher white blood cell count than the non-GC group. In subgroup analysis by age and severity, there was no significant difference in 28-day survival rate and other indicators. Compared with those in the non-GC group, patients in the GC group more frequently required admission to the intensive care unit. Conclusion In the present study, we found no significant improvement in patients with severe COVID-19 pneumonia treated with GCs within 7 days of admission.
Accessible, Transparent, Progressive: Conceptualising the Militarisation of Digital Space Through the Social Media Presence of Arms Manufacturers
Authors: Jester Natalie 
Published: February 2023

Arms sales cause serious harm and the public is – on some level – aware of this, yet their sale continues apace. Militarisation is the engendering of support for war, broadly understood, and this includes the manufacture/sale of weapons. This article examines the Twitter feeds of three large US arms manufacturers: Lockheed Martin, Raytheon and Northrop Grumman (as part of a larger project where approximately 900 tweets were examined). It argues that productive tensions of exposure (knowing) and revelation (societal acknowledgement) engender militarisation within arms manufacturers’ Twitter feeds. It finds that arms manufacturers represent themselves as accessible/transparent through regular updates and high volumes of information. They also distract from the violence of their products by presenting themselves as drivers of human progress, which occurs in social, environmental and technological dimensions. Taken as a whole, the representations of accessibility and distracting content on social media function to facilitate the arms trade in this case. Accessible, transparente, progressive : conceptualiser la militarisation de l’espace numérique à travers la présence de fabricants d’armes sur les réseaux sociaux
Strategic deviation and investment inefficiency
Authors: Ranasinghe Dinithi , Habib Ahsan 
Published: February 2023

We examine the association between strategic deviation and investment inefficiency. We conceptualize strategic deviation as the extent to which the pattern of a firm’s resource allocation deviates from its industry peers. We posit that firms pursuing deviant strategies are prone to increased information asymmetry and hence, are able to engage in self-serving behaviour as manifested in inefficient investments. Our results suggest that deviant firms have sub-optimal investments. A battery of robustness tests validates our findings. We further provide evidence to suggest that weaker monitoring, high product market competition and a low-quality information environment moderate the relation between strategic deviation and investment inefficiency. JEL Classification: M41, G41
Diagnosis of malignant pleural effusion with combinations of multiple tumor markers: A comparison study of five machine learning models
Authors: Zhang Yixi , Wang Jingyuan , Liang Baosheng , Wu Hanyu , Chen Yangyu 
Published: February 2023

Background To evaluate the diagnostic value of combinations of tumor markers carcinoembryonic antigen (CEA), carbohydrate antigen (CA) 125, CA153, and CA19-9 in identifying malignant pleural effusion (MPE) from non-malignant pleural effusion (non-MPE) using machine learning, and compare the performance of popular machine learning methods. Methods A total of 319 samples were collected from patients with pleural effusion in Beijing and Wuhan, China, from January 2018 to June 2020. Five machine learning methods including Logistic regression, extreme gradient boosting (XGBoost), Bayesian additive regression tree, random forest, and support vector machine were applied to evaluate the diagnostic performance. Sensitivity, specificity, Youden's index, and the area under the receiver operating characteristic curve (AUC) were used to evaluate the performance of different diagnostic models. Results For diagnostic models with a single tumor marker, the model using CEA, constructed by XGBoost, performed best (AUC = 0.895, sensitivity = 0.80), and the model with CA153, also by XGBoost, showed the largest specificity 0.98. Among all combinations of tumor markers, the combination of CEA and CA153 achieved the best performance (AUC = 0.921, sensitivity = 0.85) in identifying MPE under the diagnostic model constructed by XGBoost. Conclusions Diagnostic models for MPE with a combination of multiple tumor markers outperformed the models with a single tumor marker, particularly in sensitivity. Using machine learning methods, especially XGBoost, could comprehensively improve the diagnostic accuracy of MPE.