bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pandemic phase-related racial and ethnic disparities in COVID-19 positivity and outcomes among patients presenting to emergency departments during the first two pandemic waves in the USA
Authors: Khosla Shaveta , Del Rios Marina , Chisolm-Straker Makini , Bilal Saadiyah , Jang Timothy B , Wang Hao , Hartley Molly , Loo George T , d'Etienne James P , Newgard Craig D , Courtney D Mark , Choo Esther K , Lin Michelle P , Kline Jeffrey A 
Published: March 2024

BackgroundIn many countries including the USA, the UK and Canada, the impact of COVID-19 on people of colour has been disproportionately high but examination of disparities in patients presenting to ED has been limited. We assessed racial and ethnic differences in COVID-19 positivity and outcomes in patients presenting to EDs in the USA, and the effect of the phase of the pandemic on these outcomes.MethodsThis is a retrospective cohort study of adult patients tested for COVID-19 during, or 14 days prior to, the index ED visit in 2020. Data were obtained from the National Registry of Suspected COVID-19 in Emergency Care network which has data from 155 EDs across 27 US states. Hierarchical models were used to account for clustering by hospital. The outcomes included COVID-19 diagnosis, hospitalisation at index visit, subsequent hospitalisation within 30 days and 30-day mortality. We further stratified the analysis by time period (early phase: March–June 2020; late phase: July–September 2020).ResultsOf the 26 111 adult patients, 38% were non-Hispanic White (NHW), 29% Black, 20% Hispanic/Latino, 3% Asian and 10% all others; half were female. The median age was 56 years (IQR 40–69), and 53% were diagnosed with COVID-19; of those, 59% were hospitalised at index visit. Of those discharged from ED, 47% had a subsequent hospitalisation in 30 days. Hispanic/Latino patients had twice (adjusted OR (aOR) 2.3; 95% CI 1.8 to 3.0) the odds of COVID-19 diagnosis than NHW patients, after adjusting for age, sex and comorbidities. Black, Asian and other minority groups also had higher odds of being diagnosed (compared with NHW patients). On stratification, this association was observed in both phases for Hispanic/Latino patients. Hispanic/Latino patients had lower odds of hospitalisation at index visit, but when stratified, this effect was only observed in early phase. Subsequent hospitalisation was more likely in Asian patients (aOR 3.1; 95% CI 1.1 to 8.7) in comparison with NHW patients. Subsequent ED visit was more likely in Blacks and Hispanic/Latino patients in late phase.ConclusionWe found significant differences in ED outcomes that are not explained by comorbidity burden. The gap decreased but persisted during the later phase in 2020.
Novel and unusualUSP6fusion partners in aneurysmal bone cyst and their role in pathogenesis and histopathological evaluation of this disease
Authors: Balko Jan , Golas William , Kaspar Ludvik , Krskova Lenka , Strnadova Martina , Kotis Johana , Zamecnik Josef 
Published: March 2024

AimsThe purpose of this study is to report novel and unusualUSP6fusion partners in aneurysmal bone cysts (ABCs). These findings may be useful in routine diagnostics as well as in studying the biology ofUSP6-related disorders.MethodsA cohort of seven patients diagnosed with ABC examined between 2014 and 2023 at Motol University Hospital in Prague was included into this retrospective non-randomised study. All cases were analysed using histopathological evaluation, immunohistochemistry and Anchored multiplex RNA methods. Demographic characteristics and clinical data were also analysed.ResultsWe identified two novel (ZFXandIP6K2), three unusual (MEF2A, EIF1andCOL1A2) and two common (CDH11) fusion partners withUSP6gene among all seven cases of ABC.ConclusionsCases in our study were diagnosed as ABCs due to characteristic clinical and morphological presentation. However, not all cases are as self-evident, and molecular testing is necessary. The identification of these gene alterations can be useful in distinction between true ABC and ABC-like changes among many benign and malignant bone tumours.
Does sex influence the natural history of idiopathic adult-onset dystonia?
Authors: Velucci Vittorio , Idrissi Sarah , Pellicciari Roberta , Esposito Marcello , Trinchillo Assunta , Belvisi Daniele , Fabbrini Giovanni , Ferrazzano Gina , Terranova Carmen , Girlanda Paolo , Majorana Giovanni , Rizzo Vincenzo , Bono Francesco , Idone Giovanni , Laterza Vincenzo , Avanzino Laura , Di Biasio Francesca , Marchese Roberta , Castagna Anna , Ramella Marina , Lettieri Christian , Rinaldo Sara , Altavista Maria Concetta , Polidori Luigi , Bertolasi Laura , Tozzi Maria Chiara , Erro Roberto , Barone Paolo , Barbero Pierangelo , Ceravolo Roberto , Mascia Marcello Mario , Ercoli Tommaso , Muroni Antonella , Artusi Carlo Alberto , Zibetti Maurizio , Scaglione Cesa Lorella Maria , Bentivoglio Anna Rita , Cotelli Maria Sofia , Magistrelli Luca , Cossu Giovanni , Albanese Alberto , Squintani Giovanna Maddalena , Schirinzi Tommaso , Gigante Angelo Fabio , Maderna Luca , Eleopra Roberto , Pisani Antonio , Cassano Daniela , Romano Marcello , Rizzo Marina , Berardelli Alfredo , Defazio Giovanni 
Published: March 2024

BackgroundSeveral earlier studies showed a female predominance in idiopathic adult-onset dystonia (IAOD) affecting the craniocervical area and a male preponderance in limb dystonia. However, sex-related differences may result from bias inherent to study design. Moreover, information is lacking on whether sex-related differences exist in expressing other dystonia-associated features and dystonia spread.ObjectiveTo provide accurate information on the relationship between sex differences, motor phenomenology, dystonia-associated features and the natural history of IAOD.MethodsData of 1701 patients with IAOD from the Italian Dystonia Registry were analysed.ResultsWomen predominated over men in blepharospasm, oromandibular, laryngeal and cervical dystonia; the sex ratio was reversed in task-specific upper limb dystonia; and no clear sex difference emerged in non-task-specific upper limb dystonia and lower limb dystonia. This pattern was present at disease onset and the last examination. Women and men did not significantly differ for several dystonia-associated features and tendency to spread. In women and men, the absolute number of individuals who developed dystonia tended to increase from 20 to 60 years and then declined. However, when we stratified by site of dystonia onset, different patterns of female-to-male ratio over time could be observed in the various forms of dystonia.ConclusionsOur findings provide novel evidence on sex as a key mediator of IAOD phenotype at disease onset. Age-related sexual dimorphism may result from the varying exposures to specific age-related and sex-related environmental risk factors interacting in a complex manner with biological factors such as hormonal sex factors.
Major bleeding in patients with atrial fibrillation treated with apixaban versus warfarin in combination with amiodarone: nationwide cohort study
Authors: Fritz Hansson Astrid , Modica Angelo , Renlund Henrik , Christersson Christina , Held Claes , Batra Gorav 
Published: March 2024

BackgroundAmiodarone is an established treatment for atrial fibrillation (AF) but might interfere with the metabolism of apixaban or warfarin. Therefore, the aim was to investigate the occurrence of major bleeding among patients with AF treated with amiodarone in combination with apixaban or warfarin.MethodsRetrospective observational study using Swedish health registers. All patients with AF in the National Patient Register and the National Dispensed Drug Register with concomitant use of amiodarone and warfarin or apixaban between 1 June 2013 and 31 December 2018 were included. Propensity score matching was performed, and matched cohorts were compared using Cox proportional HRs. The primary outcome was major bleeding resulting in hospitalisation based on International Classification of Diseases (ICD)-10 codes. Secondary outcomes included intracranial bleeding, gastrointestinal bleeding and other bleeding. Exploratory outcomes included ischaemic stroke/systemic embolism and all-cause/cardiovascular (CV) mortality.ResultsA total of 12 103 patients met the inclusion criteria and 8686 patients were included after propensity score matching. Rates of major bleeding were similar in the apixaban (4.3/100 patient-years) and warfarin cohort (4.5/100 patient-years) (HR: 1.03; 95% CI: 0.76 to 1.39) during median follow-up of 4.4 months. Similar findings were observed for secondary outcomes including gastrointestinal bleeding and other bleeding, and exploratory outcomes including ischaemic stroke/systemic embolism and all-cause/CV mortality.ConclusionsAmong patients treated with amiodarone in combination with apixaban or warfarin, major bleeding and thromboembolic events were rare and with no significant difference between the treatment groups.EUPAS registry numberEUPAS43681.
Meta-analyses of the global multilocus genotypes of the human pathogen Campylobacter jejuni
Authors: Poorrashidi Monir , Hitchcock Megan , Xu Jianping 
Published: March 2024

Campylobacter infections are a leading cause of bacterial diarrheal illness worldwide, with increasing reports of outbreaks in both developing and developed countries. Most studies investigating strain genotypes and epidemiology of Campylobacter jejuni examined on a local scale. Using the archived multilocus sequence typing data at seven loci, and associated strain metadata from the PubMLST database, here we investigated the spatial and temporal genetic structure of the global population of C. jejuni. Our analyses revealed evidence for clonal dispersals of multiple sequence types (STs) among countries and continents. However, despite the observed clonal dispersal and that most genetic variations were found within individual geographic subpopulations, both the non-clone-corrected and clone-corrected samples showed evidence of significant genetic differentiation among national and continental subpopulations, with non-clone-corrected samples showing greater differentiation than clone-corrected samples. Phylogenetic incompatibility analyses provided evidence for recombination within each continental subpopulation. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across the samples. Temporally, multiple STs were found to persist across four decades and the five globally most common STs showed relatively stable frequencies over the last two decades. We discussed the implications of our results to food security, disease transmission, and public health management.
The development of computational methods for Feynman diagrams
Authors: Harlander Robert V. , Martinez Jean-Philippe 
Published: March 2024

AbstractOver the last 70 years, Feynman diagrams have played an essential role in the development of many theoretical predictions derived from the standard model Lagrangian. In fact, today they have become an essential and seemingly irreplaceable tool in quantum field theory calculations. In this article, we propose to explore the development of computational methods for Feynman diagrams with a special focus on their automation, drawing insights from both theoretical physics and the history of science. From the latter perspective, the article particularly investigates the emergence of computer algebraic programs, such as the pioneering , , and , designed to handle the intricate calculations associated with Feynman diagrams. This sheds light on the many challenges faced by physicists when working at higher orders in perturbation theory and reveal, as exemplified by the test of the validity of quantum electrodynamics at the turn of the 1960s and 1970s, the indispensable necessity of computer-assisted procedures. In the second part of the article, a comprehensive overview of the current state of the algorithmic evaluation of Feynman diagrams is presented from a theoretical point of view. It emphasizes the key algorithmic concepts employed in modern perturbative quantum field theory computations and discusses the achievements, ongoing challenges, and potential limitations encountered in the application of the Feynman diagrammatic method. Accordingly, we attribute the enduring significance of Feynman diagrams in contemporary physics to two main factors: the highly algorithmic framework developed by physicists to tackle these diagrams and the successful advancement of algebraic programs used to process the involved calculations associated with them.
Diffsig: Associating Risk Factors with Mutational Signatures
Authors: Park Ji-Eun , Smith Markia A. , Van Alsten Sarah C. , Walens Andrea , Wu Di , Hoadley Katherine A. , Troester Melissa A. , Love Michael I. 
Published: March 2024

Abstract

Background:
Somatic mutational signatures elucidate molecular vulnerabilities to therapy, and therefore detecting signatures and classifying tumors with respect to signatures has clinical value. However, identifying the etiology of the mutational signatures remains a statistical challenge, with both small sample sizes and high variability in classification algorithms posing barriers. As a result, few signatures have been strongly linked to particular risk factors.

Methods:
Here, we develop a statistical model, Diffsig, for estimating the association of one or more continuous or categorical risk factors with DNA mutational signatures. Diffsig takes into account the uncertainty associated with assigning signatures to samples as well as multiple risk factors' simultaneous effect on observed DNA mutations.

Results:
We applied Diffsig to breast cancer data to assess relationships between five established breast-relevant mutational signatures and etiologic variables, confirming known mechanisms of cancer development. In simulation, our model was capable of accurately estimating expected associations in a variety of contexts.

Conclusions:
Diffsig allows researchers to quantify and perform inference on the associations of risk factors with mutational signatures.

Impact:
We expect Diffsig to provide more robust associations of risk factors with signatures to lead to better understanding of the tumor development process and improved models of tumorigenesis.
Abstract A015: Multiplexed live-cell imaging for drug responses in patient-derived organoid models of endometrial cancer
Authors: Colling Kaitriana E. , Symons Emily L. , Sumanasiri Hiruni K. , Thiel Kristina W. 
Published: March 2024

Abstract
Patient-derived organoid (PDO) models of endometrial cancer are rapidly emerging as a multifunctional research model to recapitulate in vivo cancer progression and therapeutic response. PDO models are generated by reconstituting patient tumor cells in extracellular basement membrane extract (BME) and culturing as three-dimensional domes supplemented with a specialized niche of growth factors. Despite the rise in popularity of PDO models to assess drug response in vitro, there are limited commercially available reagents that are compatible with BME. In addition, most reagents are endpoint assays that require cell lysis, which is problematic because PDOs are a limited resource. Reducing drug response assessment to a single timepoint misses out on valuable kinetic response data, and samples cannot be used for subsequent downstream analyses, such as RNA sequencing or protein assays. Herein we describe a method to assess drug effects in PDO models using kinetic live-cell imaging. Live-cell imaging is a sophisticated form of automated microscopy that, when combined with fluorescent dyes, has the capacity to quantify multiple cellular responses simultaneously. Importantly, live-cell imaging reagents do not perturb cell viability or induce DNA damage, thereby allowing for accurate repeated assessment of PDO response to treatment over time. In proof-of-concept studies, we first established the utility of this approach to assess the effect of cytotoxic and cytostatic agents in PDO models of endometrial cancer. Specific parameters of interest include PDO number, area, cell health and induction of apoptosis. Agents that produced a cytotoxic effect promoted a decrease in organoid area and number over time, concomitant with an increase in apoptosis as measured by Annexin V staining. Ongoing studies are examining the dose-dependent phenotypic effects of cytostatic agents such as progestins in endometrial cancer PDO models. To evaluate the safety of the compounds, we have also conducted experiments using patient-derived organoids of normal endometrium, which was collected from uninvolved regions of the uterus in cytoreductive surgery. We envision that this automated kinetic imaging platform can be expanded to other phenotypic readouts to better understand diverse therapeutic effects of different classes of drugs under investigation for endometrial cancer.
Citation Format: Kaitriana E. Colling, Emily L. Symons, Hiruni K. Sumanasiri, Kristina W. Thiel. Multiplexed live-cell imaging for drug responses in patient-derived organoid models of endometrial cancer [abstract]. In: Proceedings of the AACR Special Conference on Endometrial Cancer: Transforming Care through Science; 2023 Nov 16-18; Boston, Massachusetts. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(5_Suppl):Abstract nr A015.
Abstract B009: Global expression analysis of endometrial cancer cells in response to progesterone identifies new therapeutic targets
Authors: Thiel Kristina , Newtson Andreea , Devor Eric , Zhang Yuping , Malmrose Paige K. , Losh Haley , Davies Suzy , Smith Lane E. , Padilla Jamie , Leiva Stephanie , Hagan Christy , Pufall Miles , Gertz Jay , Guo Yan , Leslie Kimberly K. 
Published: March 2024

Abstract
Progesterone prevents development of endometrial cancers through its receptor (PR) although the molecular mechanisms have yet to be fully characterized. In this study, we performed a global analysis of gene regulation by progesterone using human endometrial cancer cells that expressed PR endogenously or exogenously. We found progesterone strongly inhibits multiple components of the platelet derived growth factor receptor (PDGFR), Janus kinase (JAK), signal transducer and activator of transcription (STAT) pathway through PR. The PDGFR/JAK/STAT pathway signals to control numerous downstream targets including AP-1 transcription factors Fos and Jun. Treatment with inhibitors of the PDGFR/JAK/STAT pathway significantly blocked proliferation in multiple novel patient-derived organoid models of endometrial cancer, and activation of this pathway was found to be a poor prognostic signal for the survival of patients with endometrial cancer from The Cancer Genome Atlas. Our study identifies this pathway as central to the growth-limiting effects of progesterone in endometrial cancer and suggests that inhibitors of PDGFR/JAK/STAT should be considered for future therapeutic interventions.
Citation Format: Kristina Thiel, Andreea Newtson, Eric Devor, Yuping Zhang, Paige K. Malmrose, Haley Losh, Suzy Davies, Lane E. Smith, Jamie Padilla, Stephanie Leiva, Christy Hagan, Miles Pufall, Jay Gertz, Yan Guo, Kimberly K. Leslie. Global expression analysis of endometrial cancer cells in response to progesterone identifies new therapeutic targets [abstract]. In: Proceedings of the AACR Special Conference on Endometrial Cancer: Transforming Care through Science; 2023 Nov 16-18; Boston, Massachusetts. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(5_Suppl):Abstract nr B009.
Abstract B022: Conversion from minimally invasive surgical approaches to open surgery among endometrial cancer patients in a national cancer patients’ registry
Authors: Yousif Abdelrahman , Ngo Julie , Abdel-Gadir Deena , Lachance Jenny , Mize Benjamin , Chefetz Ilana 
Published: March 2024

Abstract
Endometrial cancer (EC) ranks as the predominant gynecological malignancy in the US. While minimally invasive surgical (MIS) techniques have revolutionized EC management, conversion to laparotomy remains a concern, with reported rates varying widely. Factors influencing this conversion, including patient characteristics and tumor attributes, have not been fully understood. Addressing this gap, our study employs a national registry to analyze patient, tumor, and surgeon-related factors contributing to the transition from MIS to laparotomy in EC cases. Results: 0ur results showed, 3.4% (135/4028) experienced planned MIS-to-open conversion. Demographic disparities were absent between conversion and MIS groups. Conversion was more prevalent in obese (29%) and morbidly obese (37%) patients (P=0.04), linked to prior abdominal surgery (63% vs 52%; P=0.001). Endometrioid EC predominated (59%) in the converted group, with higher non-endometrioid rates (serous carcinoma 16%, clear cell carcinoma 4%, carcinosarcoma 5%, mixed histology 12%; all P&lt;0.01). Advanced FIGO stages were more common in conversions (stage II: 5%, stage III: 25%, stage IV: 9%; all P&lt;0.001). Type II (24%) and type III (5%) hysterectomies were more frequent in conversions (P&lt;0.001). Logistic regression indicated BMI, prior surgery, FIGO stage, histology, and operation type affected conversion (p&lt;0.001), explaining 12.3% of variance. Indications for conversion included uterine size, adhesions, and disease extent. Conclusion: the adoption of minimally invasive surgery (MIS) has become increasingly popular for managing endometrial cancer (EC), attributed to enhanced perioperative outcomes. However, prudent patient selection and surgical planning are imperative to mitigate the risk of unplanned transition to open surgery. Predictive factors for such conversion include uterine size, prior abdominal surgeries, surgical complexity, disease extent, and histologic types. Further prospective research is warranted to validate these findings and identify individuals at conversion risk. Ultimately, a personalized surgical approach, tailored to individual patient attributes, remains pivotal for optimizing outcomes in EC management.
Citation Format: Abdelrahman Yousif, Julie Ngo, Deena Abdel-Gadir, Jenny Lachance, Benjamin Mize, Ilana Chefetz. Conversion from minimally invasive surgical approaches to open surgery among endometrial cancer patients in a national cancer patients’ registry [abstract]. In: Proceedings of the AACR Special Conference on Endometrial Cancer: Transforming Care through Science; 2023 Nov 16-18; Boston, Massachusetts. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(5_Suppl):Abstract nr B022.