bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Nrf2-OSGIN1&2-HSP70 axis mediates cigarette smoke-induced endothelial detachment: implications for plaque erosion
Authors: Satta Sandro , Beal Robert , Smith Rhys , Luo Xing , Ferris Glenn R , Langford-Smith Alex , Teasdale Jack , Ajime Tom Tanjeko , Serré Jef , Hazell Georgina , Newby Graciela Sala , Johnson Jason L , Kurinna Svitlana , Humphries Martin J , Gayan-Ramirez Ghislaine , Libby Peter , Degens Hans , Yu Bo , Johnson Thomas , Alexander Yvonne , Jia Haibo , Newby Andrew C , White Stephen J 
Published: February 2023

Abstract

Aims
Endothelial erosion of plaques is responsible for ∼30% of acute coronary syndromes (ACS). Smoking is a risk factor for plaque erosion, which most frequently occurs on the upstream surface of plaques where the endothelium experiences elevated shear stress. We sought to recreate these conditions in vitro to identify potential pathological mechanisms that might be of relevance to plaque erosion.

Methods and results
Culturing human coronary artery endothelial cells (HCAECs) under elevated flow (shear stress of 7.5 Pa) and chronically exposing them to cigarette smoke extract (CSE) and tumour necrosis factor-alpha (TNFα) recapitulated a defect in HCAEC adhesion, which corresponded with augmented Nrf2-regulated gene expression. Pharmacological activation or adenoviral overexpression of Nrf2 triggered endothelial detachment, identifying Nrf2 as a mediator of endothelial detachment. Growth/Differentiation Factor-15 (GDF15) expression was elevated in this model, with protein expression elevated in the plasma of patients experiencing plaque erosion compared with plaque rupture. The expression of two Nrf2-regulated genes, OSGIN1 and OSGIN2, was increased by CSE and TNFα under elevated flow and was also elevated in the aortas of mice exposed to cigarette smoke in vivo. Knockdown of OSGIN1&2 inhibited Nrf2-induced cell detachment. Overexpression of OSGIN1&2 induced endothelial detachment and resulted in cell cycle arrest, induction of senescence, loss of focal adhesions and actin stress fibres, and disturbed proteostasis mediated in part by HSP70, restoration of which reduced HCAEC detachment. In ACS patients who smoked, blood concentrations of HSP70 were elevated in plaque erosion compared with plaque rupture.

Conclusion
We identified a novel Nrf2-OSGIN1&2-HSP70 axis that regulates endothelial adhesion, elevated GDF15 and HSP70 as biomarkers for plaque erosion in patients who smoke, and two therapeutic targets that offer the potential for reducing the risk of plaque erosion.
Migration of stem-like CD8 T cells between tissue microenvironments underpins successful anti-tumour immune responses
Authors: Kennedy Bethany C , Dean Isaac , Withers David R 
Published: February 2023

SummaryThe clinical success of immune checkpoint blockade in some patients has transformed treatment approaches in cancer and offers the hope of durable curative responses. Building from studies of chronic infection, the composition of tumour infiltrating lymphocytes and in particular, the spectrum of exhausted CD8 T cells has now been characterized in detail, profiling the phenotype, function, transcriptional regulation and even the epigenetic changes. However, what remains less clear is how intratumoural immune cells interface with populations in the periphery, both in terms of sustaining the response in cancer, but also in establishing systemic memory responses that can provide long-term protection. Here we will succinctly review the current understanding of the anti-tumour response, consider the tissue microenvironments that support key cellular subsets and the extent to which cellular migration between these sites impacts the response.
Osmia taurus (Hymenoptera: Megachilidae): A Non-native Bee Species With Invasiveness Potential in North America
Authors: Gutierrez Grace M , LeCroy Kathryn A , Roulston T’ai H , Biddinger David J , López-Uribe Margarita M 
Published: February 2023

Abstract
Bees are important pollinators and are essential for the reproduction of many plants in natural and agricultural ecosystems. However, bees can have adverse ecological effects when introduced to areas outside of their native geographic ranges. Dozens of non-native bee species are currently found in North America and have raised concerns about their potential role in the decline of native bee populations. Osmia taurus Smith (Hymenoptera: Megachilidae) is a mason bee native to eastern Asia that was first reported in the United States in 2002. Since then, this species has rapidly expanded throughout the eastern part of North America. Here, we present a comprehensive review of the natural history of O. taurus, document its recent history of spread through the United States and Canada, and discuss the evidence suggesting its potential for invasiveness. In addition, we compare the biology and history of colonization of O. taurus to O. cornifrons (Radoszkowski), another non-native mason bee species now widespread in North America. We highlight gaps of knowledge and future research directions to better characterize the role of O. taurus in the decline of native Osmia spp. Panzer and the facilitation of invasive plant-pollinator mutualisms.
The right age for the en-bloc rotation of the outflow tracts: a single-centre experience
Authors: Kreuzer Michaela , Sames-Dolzer Eva , Tulzer Andreas , Gierlinger Gregor , Mair Roland , Nawrozi Mohammad-Paimann , Mair Rudolf 
Published: February 2023

Abstract

OBJECTIVES
The en-bloc rotation of the outflow tracts (EBR) enables an anatomic correction of transposition of the great arteries with ventricular septal defect and left ventricular outflow tract obstruction. The anatomical condition or previous palliative procedures may allow choosing an elective date for the anatomic correction. The aim of this study was to evaluate the optimal age for performing the EBR based on the largest series published so far.

METHODS
At the Children’s Heart Center Linz, the EBR was performed in 33 patients between 2003 and 2021. Median age at operation was 74 [interquartile range (IQR) 17–627] days. Twelve patients were newborns (≤28 days), 9 older than 369 days. These 2 groups were compared to the remaining patients each regarding peri- and postoperative data, complications, reinterventions and mortality. The median follow-up period was 5.4 (IQR 0.99–11.74) years.

RESULTS
In-hospital mortality was 6.1%. All-cause mortality was lower in patients younger than 369 days at the time of EBR (4.2% vs 44.4% in patients &gt;369 days old, P = 0.013). In newborns, intensive care unit stay (median 18.5 days vs 8 days, P = 0.008) and in-hospital stay (median 29.5 days vs 15 days, P = 0.026) were significantly longer, the risk for postoperative AV block was higher (33.3 vs 0%, P = 0.012) than in patients who had been corrected anatomically after the neonatal period.

CONCLUSIONS
The results of this study suggest the deferral of the EBR to the post-newborn period. A significantly higher mortality rate in patients of older age at operation seems to recommend the anatomic correction during the first year of life.
Association Between Cognitive Impairment and Repeat Fractures in Medicare Beneficiaries Recently Hospitalized for Hip Fracture
Authors: Tzeng Huey-Ming , Downer Brian , Li Chih-Ying , Raji Mukaila A , Haas Allen , Kuo Yong-Fang 
Published: February 2023

Abstract

Background
Repeat fractures contribute substantially to fracture incidents in older adults. We examined the association between cognitive impairment and re-fractures during the first 90 days after older adults with hip fractures were discharged home from a skilled nursing facility rehabilitation short stay.

Methods
Multilevel binary logistic regression was used to analyze 100% of U.S. national postacute-care fee-for-service Medicare beneficiaries who had a hospital admission for hip fracture from January 1, 2018, to July 31, 2018; were admitted for a skilled nursing facility stay within 30 days of hospital discharge; and were discharged to the community after a short stay. Our primary outcome was rehospitalization for any re-fractures within 90 days of skilled nursing facility discharge. Cognitive status assessed at skilled nursing facility admission or before discharge was classified as either intact or having mild or moderate/severe impairment.

Results
In 29 558 beneficiaries with hip fracture, odds of any re-fracture were higher in those with minor (odds ratio: 1.48; 95% confidence interval: 1.19–1.85; p &lt; .01) and moderate/major cognitive impairment (odds ratio: 1.42; 95% confidence interval: 1.07–1.89; p = .0149) than in those classified as intact.

Conclusions
Beneficiaries with cognitive impairment were more likely than their counterparts with no cognitive impairment to experience re-fractures. Community-dwelling older adults with minor cognitive impairment may experience a higher likelihood of experiencing a repeat fracture leading to rehospitalization.
Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows
Authors: Suetake Hirotaka , Fukusato Tsukasa , Igarashi Takeo , Ohta Tazro 
Published: February 2023

AbstractBackgroundMany open-source workflow systems have made bioinformatics data analysis procedures portable. Sharing these workflows provides researchers easy access to high-quality analysis methods without the requirement of computational expertise. However, published workflows are not always guaranteed to be reliably reusable. Therefore, a system is needed to lower the cost of sharing workflows in a reusable form.ResultsWe introduce Yevis, a system to build a workflow registry that automatically validates and tests workflows to be published. The validation and test are based on the requirements we defined for a workflow being reusable with confidence. Yevis runs on GitHub and Zenodo and allows workflow hosting without the need of dedicated computing resources. A Yevis registry accepts workflow registration via a GitHub pull request, followed by an automatic validation and test process for the submitted workflow. As a proof of concept, we built a registry using Yevis to host workflows from a community to demonstrate how a workflow can be shared while fulfilling the defined requirements.ConclusionsYevis helps in the building of a workflow registry to share reusable workflows without requiring extensive human resources. By following Yevis’s workflow-sharing procedure, one can operate a registry while satisfying the reusable workflow criteria. This system is particularly useful to individuals or communities that want to share workflows but lacks the specific technical expertise to build and maintain a workflow registry from scratch.
Protection From COVID-19 mRNA Vaccination and Prior SARS-CoV-2 Infection Against COVID-19–Associated Encounters in Adults During Delta and Omicron Predominance
Authors: Bozio Catherine H , Butterfield Kristen A , Briggs Hagen Melissa , Grannis Shaun , Drawz Paul , Hartmann Emily , Ong Toan C , Fireman Bruce , Natarajan Karthik , Dascomb Kristin , Gaglani Manjusha , DeSilva Malini B , Yang Duck-Hye , Midgley Claire M , Dixon Brian E , Naleway Allison L , Grisel Nancy , Liao I Chia , Reese Sarah E , Fadel William F , Irving Stephanie A , Lewis Ned , Arndorfer Julie , Murthy Kempapura , Riddles John , Valvi Nimish R , Mamawala Mufaddal , Embi Peter J , Thompson Mark G , Stenehjem Edward 
Published: February 2023

Abstract

Background
Data assessing protection conferred from COVID-19 mRNA vaccination and/or prior SARS-CoV-2 infection during Delta and Omicron predominance periods in the United States are limited.

Methods
This cohort study included persons ≥18 years who had ≥1 health care encounter across 4 health systems and had been tested for SARS-CoV-2 before 26 August 2021. COVID-19 mRNA vaccination and prior SARS-CoV-2 infection defined the exposure. Cox regression estimated hazard ratios (HRs) for the Delta and Omicron periods; protection was calculated as (1−HR)×100%.

Results
Compared to unvaccinated and previously uninfected persons, during Delta predominance, protection against COVID-19–associated hospitalizations was high for those 2- or 3-dose vaccinated and previously infected, 3-dose vaccinated alone, and prior infection alone (range, 91%–97%, with overlapping 95% confidence intervals [CIs]); during Omicron predominance, estimates were lower (range, 77%–90%). Protection against COVID-19–associated emergency department/urgent care (ED/UC) encounters during Delta predominance was high for those exposure groups (range, 86%–93%); during Omicron predominance, protection remained high for those 3-dose vaccinated with or without a prior infection (76%; 95% CI = 67%–83% and 71%; 95% CI = 67%–73%, respectively).

Conclusions
COVID-19 mRNA vaccination and/or prior SARS-CoV-2 infection provided protection against COVID-19–associated hospitalizations and ED/UC encounters regardless of variant. Staying up-to-date with COVID-19 vaccination still provides protection against severe COVID-19 disease, regardless of prior infection.
The Estimated Lifetime Quality-Adjusted Life-Years Lost Due to Chlamydia, Gonorrhea, and Trichomoniasis in the United States in 2018
Authors: Li Yunfei , You Shiying , Lee Kyueun , Yaesoubi Reza , Hsu Katherine , Gift Thomas L , Chesson Harrell W , Berruti Andrés A , Salomon Joshua A , Rönn Minttu M 
Published: February 2023

Abstract

Background
Comprehensive evaluation of the quality-adjusted life-years (QALYs) lost attributable to chlamydia, gonorrhea, andtrichomoniasis in the United States is lacking.

Methods
We adapted a previous probability-tree model to estimate the average number of lifetime QALYs lost due to genital chlamydia, gonorrhea, and trichomoniasis, per incident infection and at the population level, by sex and age group. We conducted multivariate sensitivity analyses to address uncertainty around key parameter values.

Results
The estimated total discounted lifetime QALYs lost for men and women, respectively, due to infections acquired in 2018, were 1541 (95% uncertainty interval [UI], 186–6358) and 111 872 (95% UI, 29 777–267 404) for chlamydia, 989 (95% UI, 127–3720) and 12 112 (95% UI, 2 410–33 895) for gonorrhea, and 386 (95% UI, 30–1851) and 4576 (95% UI, 13–30 355) for trichomoniasis. Total QALYs lost were highest among women aged 15–24 years with chlamydia. QALYs lost estimates were highly sensitive to disutilities (health losses) of infections and sequelae, and to duration of infections and chronic sequelae for chlamydia and gonorrhea in women.

Conclusions
The 3 sexually transmitted infections cause substantial health losses in the United States, particularly gonorrhea and chlamydia among women. The estimates of lifetime QALYs lost per infection help to prioritize prevention policies and inform cost-effectiveness analyses of sexually transmitted infection interventions.
Biochemical characterization of the RNA-binding and RNA–DNA strand exchange activities of the human RAD52 protein
Authors: Tsuchiya Ryohei , Saotome Mika , Kinoshita Chiaki , Kamoi Kazuki , Kagawa Wataru 
Published: February 2023

Summary
RAD52 is a single-stranded DNA (ssDNA) binding protein that functions in the repair of DNA double-strand breaks (DSBs) by promoting the annealing of complementary DNA strands. RAD52 may also play an important role in an RNA transcript-dependent type of DSB repair, in which it reportedly binds to RNA and mediates the RNA–DNA strand exchange reaction. However, the mechanistic details of these functions are still unclear. In the present study, we utilized the domain fragments of RAD52 to biochemically characterize the single-stranded RNA (ssRNA) binding and RNA–DNA strand exchange activities of RAD52. We found that the N-terminal half of RAD52 is primarily responsible for both activities. By contrast, significant differences were observed for the roles of the C-terminal half in RNA–DNA and DNA–DNA strand exchange reactions. The C-terminal fragment stimulated the inverse RNA–DNA strand exchange activity displayed by the N-terminal fragment in trans, whereas the trans stimulatory effect by the C-terminal fragment was not observed in the inverse DNA–DNA or forward RNA–DNA strand exchange reactions. These results suggest the specific function of the C-terminal half of RAD52 in RNA-templated DSB repair.
Testicular choriocarcinoma: a rare diagnosis in a patient presenting with hemorrhagic shock
Authors: Mazzeo Michael , Bhattacharyya Ratul , Yang James , Molavi Ida 
Published: February 2023

AbstractTesticular choriocarcinoma is a rare and aggressive subtype of nonseminomatous germ cell tumors accounting for &lt;1% of all germ cell tumors. We report an unusual case of testicular choriocarcinoma metastasis that presents as hemorrhagic shock. Diagnosis was unsuspected and difficult with vast other potential causes. This case highlights the importance of proper foundational workup and management that ultimately led to the appropriate definitive treatment of unusual manifestations of undiagnosed metastatic choriocarcinoma in a critical patient.
Singular spectrum analysis of time series data from low-frequency radiometers, with an application to SITARA data
Authors: Thekkeppattu Jishnu N , Trott Cathryn M , McKinley Benjamin 
Published: February 2023

ABSTRACT
Understanding the temporal characteristics of data from low-frequency radio telescopes is of importance in devising suitable calibration strategies. Application of time-series analysis techniques to data from radio telescopes can reveal a wealth of information that can aid in calibration. In this paper, we investigate singular spectrum analysis (SSA) as an analysis tool for radio data. We show the intimate connection between SSA and Fourier techniques. We develop the relevant mathematics starting with an idealized periodic dataset and proceeding to include various non-ideal behaviours. We propose a novel technique to obtain long-term gain changes in data, leveraging the periodicity arising from sky drift through the antenna beams. We also simulate several plausible scenarios and apply the techniques to a 30-day time series data collected during 2021 June from SITARA – a short-spacing two element interferometer for global 21-cm detection. Applying the techniques to real data, we find that the first reconstructed component – the trend – has a strong anti-correlation with the local temperature suggesting temperature fluctuations as the most likely origin for the observed variations in the data. We also study the limitations of the calibration in the presence of diurnal gain variations and find that such variations are the likely impediment to calibrating SITARA data with SSA.
Identifying anomalous radio sources in the Evolutionary Map of the Universe Pilot Survey using a complexity-based approach
Authors: Segal Gary , Parkinson David , Norris Ray , Hopkins Andrew M , Andernach Heinz , Alexander Emma L , Carretti Ettore , Koribalski Bärbel S , Legodi Letjatji S , Leslie Sarah , Luo Yan , Pierce Jonathon C S , Tang Hongming , Vardoulaki Eleni , Vernstrom Tessa 
Published: February 2023

ABSTRACTThe Evolutionary Map of the Universe (EMU) large-area radio continuum survey will detect tens of millions of radio galaxies, giving an opportunity for the detection of previously unknown classes of objects. To maximize the scientific value and make new discoveries, the analysis of these data will need to go beyond simple visual inspection. We propose the coarse-grained complexity, a simple scalar quantity relating to the minimum description length of an image that can be used to identify unusual structures. The complexity can be computed without reference to the broader sample or existing catalogue data, making the computation efficient on new surveys at very large scales (such as the full EMU survey). We apply our coarse-grained complexity measure to data from the EMU Pilot Survey to detect and confirm anomalous objects in this data set and produce an anomaly catalogue. Rather than work with existing catalogue data using a specific source detection algorithm, we perform a blind scan of the area, computing the complexity using a sliding square aperture. The effectiveness of the complexity measure for identifying anomalous objects is evaluated using crowd-sourced labels generated via the Zooniverse.org platform. We find that the complexity scan identifies unusual sources, such as odd radio circles, by partitioning on complexity. We achieve partitions where 5 per cent of the data is estimated to be 86 per cent complete, and 0.5 per cent is estimated to be 94 per cent pure, with respect to anomalies and use this to produce an anomaly catalogue.
Preservation of the Innate Immune Response toClostridioides difficileInfection in Hospitalized Immunocompromised Patients
Authors: Banegas Marcela , Villafuerte-Gálvez Javier , Paredes Rodrigo , Sprague Rebecca , Barrett Caitlin , Gonzales-Luna Anne J , Daugherty Kaitlyn , Garey Kevin W , Xu Hua , Lin Qianyun , Wang Lamei , Chen Xinhua , Pollock Nira R , Kelly Ciarán P , Alonso Carolyn D 
Published: February 2023

AbstractBackgroundClostridioides difficile infection (CDI) immune response is influenced by the innate and adaptive (humoral) immune systems. Our prior research found attenuated humoral responses to C difficile in immunocompromised hosts (ICHs) with CDI. We sought to evaluate whether the innate immune response to CDI was influenced by ICH status.MethodsWe conducted a prospective study of hospitalized adults with CDI (acute diarrhea, positive C difficile stool nucleic acid amplification testing [NAAT], and decision to treat), with and without immunosuppression and measured a panel of cytokines (granulocyte colony-stimulating factor [G-CSF], interleukin [IL]–10, IL-15, IL-1β, IL-4, IL-6, IL-8, and tumor necrosis factor–α) in blood and stool at CDI diagnosis. Results were compared with measurements from a cohort of asymptomatic carrier patients (ASCs) (NAAT positive, without diarrhea) with and without immunocompromise.ResultsOne hundred twenty-three subjects (42 ICHs, 50 non-ICHs, 31 ASCs) were included. Median values for blood and stool cytokines were similar in ICH versus non-ICH CDI subjects. In blood, G-CSF, IL-10, IL-15, IL-6, and IL-8 were higher in both groups of CDI subjects versus the ASC cohort (P &lt; .05). In stool, IL-1β and IL-8 were higher in both groups of CDI subjects versus the ASC cohort (P &lt; .05). Median stool concentrations of IL-1β demonstrated significant differences between the groups (ICHs, 10.97 pg/mL; non-ICHs, 9.71 pg/mL; and ASCs, 0.56 pg/mL) (P &lt; .0001).ConclusionsIn this small exploratory analysis, ICH status did not significantly impact blood and fecal patterns of cytokines in humans at the diagnosis of CDI, suggesting that the innate immune response to C difficile may be conserved in immunocompromised patients.