bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 in Pregnancy and Early Childhood (COPE): study protocol for a prospective, multicentre biobank, survey and database cohort study
Authors: Carlsson Ylva , Bergman Lina , Zaigham Mehreen , Linden Karolina , Andersson Ola , Veje Malin , Sandström Anna , Wikström Anna-Karin , Östling Hanna , Fadl Helena , Domellöf Magnus , Blomberg Marie , Brismar Wendel Sophia , Åden Ulrika , Sengpiel Verena 
Published: September 2021

IntroductionThere is limited knowledge on how the SARS-CoV-2 affects pregnancy outcomes. Studies investigating the impact of COVID-19 in early pregnancy are scarce and information on long-term follow-up is lacking.The purpose of this project is to study the impact of COVID-19 on pregnancy outcomes and long-term maternal and child health by: (1) establishing a database and biobank from pregnant women with COVID-19 and presumably non-infected women and their infants and (2) examining how women and their partners experience pregnancy, childbirth and early parenthood in the COVID-19 pandemic.Methods and analysisThis is a national, multicentre, prospective cohort study involving 27 Swedish maternity units accounting for over 86 000 deliveries/year. Pregnant women are included when they: (1) test positive for SARS-CoV-2 (COVID-19 group) or (2) are non-infected and seek healthcare at one of their routine antenatal visits (screening group). Blood, as well as other biological samples, are collected at different time points during and after pregnancy. Child health up to 4 years of age and parent experience of pregnancy, delivery, early parenthood, healthcare and society in general will be examined using web-based questionnaires based on validated instruments. Short- and long-term health outcomes will be collected from Swedish health registers and the parents’ experiences will be studied by performing qualitative interviews.Ethics and disseminationConfidentiality aspects such as data encryption and storage comply with the General Data Protection Regulation and with ethical committee requirements. This study has been granted national ethical approval by the Swedish Ethical Review Authority (dnr 2020-02189 and amendments 2020-02848, 2020-05016, 2020-06696 and 2021-00870) and national biobank approval by the Biobank Väst (dnr B2000526:970). Results from the project will be published in peer-reviewed journals.Trial registration numberNCT04433364.
Protocol for the economic evaluation of COVID-19 pandemic response policies
Authors: Chua Brandon Wen Bing , Huynh Vinh Anh , Lou Jing , Goh Fang Ting , Clapham Hannah , Teerawattananon Yot , Wee Hwee Lin 
Published: September 2021

IntroductionSeveral treatment options are available for COVID-19 to date. However, the use of a combination of non-pharmaceutical interventions (NPIs) is necessary for jurisdictions to contain its spread. Although the implementation cost of NPIs may be low from the healthcare system perspective, it can be costly when considering the indirect costs from the societal perspective. COVID-19 vaccination campaigns have begun in several countries worldwide. Nonetheless, the quantity of vaccines available remain limited over the next 1 to 2 years. A tool for informing vaccine prioritisation that considers both cost and effectiveness will be highly useful. This study aims to identify the most cost-effective combination of COVID-19 response policies, using Singapore as an example.Methods and analysisAn age-stratified Susceptible-Exposed-Infectious-Recovered model will be used to generate the number of infections stratified by disease severity under different intervention scenarios. Polices of interest include test-trace-isolate, travel restriction, compulsory face mask and hygiene practices, social distancing, dexamethasone/remdesivir therapy and vaccination. The latest phase 3 trial results and the WHO Target Product Profiles for COVID-19 vaccines will be used to model vaccine characteristics. A cost (expected resource utilisation and productivity losses) and quality-adjusted life years (QALYs) will be attached to these outputs for a cost-utility analysis. The primary outcome measure will be the incremental cost-effectiveness ratio generated from the incremental cost of policy alternatives expressed as a ratio of the incremental benefits (QALYs gained). Efficacy of policy options will be gathered from literature review and from its observed impacts in Singapore. Cost data will be gathered from healthcare institutions, Ministry of Health and published data. Sensitivity analysis such as threshold analysis and scenario analysis will be conducted.Ethics and disseminationEthics approval was not required for this study. The study findings will be disseminated through peer-reviewed journals.
Patterns of compliance with COVID-19 preventive behaviours: a latent class analysis of 20 000 UK adults
Authors: Wright Liam , Steptoe Andrew , Fancourt Daisy 
Published: September 2021

BackgroundGovernments have implemented a range of measures to tackle COVID-19, primarily focusing on changing citizens’ behaviours in order to lower the transmission of the virus. Few studies have looked at the patterns of compliance with different measures within individuals: whether people comply with all measures or selectively choose some but not others. Such research is important for designing interventions to increase compliance.MethodsWe used cross-sectional data from 20 947 UK adults in the COVID-19 Social Study collected from 17 November to 23 December 2020. Self-report compliance was assessed with six behaviours: mask wearing, hand washing, indoor household mixing, outdoor household mixing, social distancing and compliance with other guidelines. Patterns of compliance behaviour were identified using latent class analysis, and multinomial logistic regression was used to assess demographic, socioeconomic and personality predictors of behaviour patterns.ResultsWe selected a four-latent class solution. Most individuals reported similar levels of compliance across the six behaviour measures. High level of compliance was the modal response. Lower self-reported compliance was related to young age, high risk-taking behaviour, low confidence in government and low empathy, among other factors. Looking at individual behaviours, mask wearing had the highest level of compliance while compliance with social distancing was relatively low.ConclusionResults suggest that individuals choose to comply with all guidelines, rather than some but not others. Strategies to increase compliance should focus on increasing general motivations to comply alongside specifically encouraging social distancing.
Risk of tuberculosis in patients with cancer treated with immune checkpoint inhibitors: a nationwide observational study
Authors: Bae Seongman , Kim Ye-Jee , Kim Min-ju , Kim Jwa Hoon , Yun Sung-Cheol , Jung Jiwon , Kim Min Jae , Chong Yong Pil , Kim Sung-Han , Choi Sang-Ho , Kim Yang Soo , Lee Sang-Oh 
Published: September 2021

BackgroundWhile some recent studies have reported the development of tuberculosis (TB) in patients exposed to immune checkpoint inhibitors (ICIs), there is limited evidence to date. Therefore, we evaluated the risk of TB in patients with cancer exposed to ICIs using the National Health Insurance claims data in South Korea.MethodsPatients with diagnostic codes for non-small cell lung cancer, urothelial carcinoma or melanoma between August 2017 and June 2019 were identified. The incidence rate and standardized incidence ratio (SIR) of TB were calculated for both the ICI exposure and non-exposure groups. The risk of TB according to ICI exposure was assessed using a multivariable Cox regression model.ResultsDuring the study period, 141 550 patients with cancer and 916 new TB cases were identified. Among the 5037 patients exposed to ICIs, 20 were diagnosed with TB at a median of 2.2 months after the ICI was initiated. The crude incidence rate of TB per 100,000 person-years was 675.8 (95% CI 412.8 to 1043.8) for the ICI exposure group and 599.1 (95% CI 560.5 to 639.6) for the non-exposure group. The SIR for TB was 8.1 (95% CI 8.0 to 8.2) in the ICI exposure group. After adjusting for potential confounding factors, ICI treatment was not significantly associated with an increased risk of TB (HR: 0.73; 95% CI 0.47 to 1.14).ConclusionsWhile the incidence of TB in cancer patients exposed to ICIs was eightfold higher than in the general population, the risk of patients with cancer developing TB did not significantly differ according to ICI exposure.
Higher blood high density lipoprotein and apolipoprotein A1 levels are associated with reduced risk of developing amyotrophic lateral sclerosis
Authors: Thompson Alexander G , Talbot Kevin , Turner Martin R 
Published: September 2021

BackgroundPremorbid body mass index, physical activity, diabetes and cardiovascular disease have been associated with an altered risk of developing amyotrophic lateral sclerosis (ALS). There is evidence of shared genetic risk between ALS and lipid metabolism. A very large prospective longitudinal population cohort permits the study of a range of metabolic parameters and the risk of subsequent diagnosis of ALS.MethodsThe risk of subsequent ALS diagnosis in those enrolled prospectively to the UK Biobank (n=502 409) was examined in relation to baseline levels of blood high and low density lipoprotein (HDL, LDL), total cholesterol, total cholesterol:HDL ratio, apolipoproteins A1 and B (apoA1, apoB), triglycerides, glycated haemoglobin A1c (HbA1c) and creatinine, plus self-reported exercise and body mass index.ResultsControlling for age and sex, higher HDL (HR 0.84, 95% CI 0.73 to 0.96, p=0.010) and apoA1 (HR 0.83, 95% CI 0.72 to 0.94, p=0.005) were associated with a reduced risk of ALS. Higher total cholesterol:HDL was associated with an increased risk of ALS (HR 1.17, 95% CI 1.05 to 1.31, p=0.006). In models incorporating multiple metabolic markers, higher LDL or apoB was associated with an increased risk of ALS, in addition to a lower risk with higher HDL or apoA. Coronary artery disease, cerebrovascular disease and increasing age were also associated with an increased risk of ALS.ConclusionsThe association of HDL, apoA1 and LDL levels with risk of ALS contributes to an increasing body of evidence that the premorbid metabolic landscape may play a role in pathogenesis. Understanding the molecular basis for these changes will inform presymptomatic biomarker development and therapeutic targeting.
Disease and economic burden increase with systemic lupus erythematosus severity 1 year before and after diagnosis: a real-world cohort study, United States, 2004–2015
Authors: Jiang Miao , Near Aimee M , Desta Barnabas , Wang Xia , Hammond Edward R 
Published: September 2021

ObjectiveTo assess the economic burden of patients with SLE by disease severity in the USA 1 year before and after diagnosis.MethodsPatients aged ≥18 years with a first SLE diagnosis (index date) between January 2005 and December 2014 were identified from administrative commercial claims data linked to electronic medical records (EMRs). Disease severity during the year after diagnosis was classified as mild, moderate, or severe using claims-based algorithms and EMR data. Healthcare resource utilisation (HCRU) and all-cause healthcare costs (2017 US$) were reported for 1 year pre-diagnosis and post-diagnosis. Generalised linear modelling examined all-cause costs over 1 year post-index, adjusting for baseline demographics, clinical characteristics, Charlson Comorbidity Index and 1 year pre-diagnosis costs.ResultsAmong 2227 patients, 26.3% had mild, 51.0% moderate and 22.7% severe SLE. Mean per-patient costs were higher for patients with moderate and severe SLE compared with mild SLE during the year before diagnosis: mild US$12 373, moderate $22 559 and severe US$39 261 (p<0.0001); and 1-year post-diagnosis period: mild US$13 415, moderate US$29 512 and severe US$68 260 (p<0.0001). Leading mean cost drivers were outpatient visits (US$13 566) and hospitalisations (US$10 252). Post-diagnosis inpatient utilisation (≥1 stay) was higher for patients with severe (51.2%) and moderate (22.4%) SLE, compared with mild SLE (12.8%), with longer mean hospital stays: mild 0.47 days, moderate 1.31 days and severe 5.52 days (p<0.0001).ConclusionHCRU and costs increase with disease severity in the year before and after diagnosis; leading cost drivers post-diagnosis were outpatient visits and hospitalisations. Earlier diagnosis and treatment may improve health outcomes and reduce HCRU and costs.
Characteristics and in-hospital outcomes of patients undergoing balloon pulmonary angioplasty for chronic thromboembolic pulmonary hypertension: a time-trend analysis from the Japanese nationwide registry
Authors: Minatsuki Shun , Takahara Mitsuyoshi , Kiyosue Arihiro , Kodera Satoshi , Hatano Masaru , Ando Jiro , Kohsaka Shun , Ishii Hideki , Shinke Toshiro , Amano Tetsuya , Ikari Yuji , Komuro Issei 
Published: September 2021

BackgroundBalloon pulmonary angioplasty (BPA), a novel technique initially introduced as a treatment for inoperable chronic thromboembolic pulmonary hypertension, is now increasingly being performed in a broader spectrum of patients. Here, we performed a time-trend analysis of the characteristics and in-hospital outcomes of patients who underwent BPA in Japan, using data extracted from nationwide procedure-based registration system.MethodsThe Japanese Structural Heart Disease (J-SHD) registry was established and sponsored by the Japanese Association of Cardiovascular Intervention and Therapeutics and aims to provide basic statistics on the performance of structural interventions in Japan. J-SHD registers cases from approximately 200 institutions, representing more than 90% of SHD intervention-performing hospitals in the nation. We analysed the registered BPA data elements from January 2015 to December 2018. Successful BPA was defined as a session in which a physician successfully treated all targeted lesions.ResultsThere were a total of 2512 BPA sessions; the number of institutions and registered sessions increased from 30 to 50 sites and from 479 to 852 sessions during the study period, respectively. The average age of the patients was 66±13 years, and 72.1% were women. In-hospital death was observed in 0.2%, and the total complications rate was 5.3%. The preoperative and postoperative mean pulmonary artery pressure were 32±11 mm Hg and 30±10 mm Hg, respectively.ConclusionThe number of BPA sessions increased during the study period, with an acceptable in-hospital complication rate.
Invasion of Celtis tala forests by Ligustrum lucidum in Argentina: impact on soil properties and the arbuscular mycorrhizal fungi community
Authors: Abarca Camila , Barrera Marcelo , Arturi Marcelo , Allegrucci Natalia , Velázquez María Silvana 
Published: September 2021

The arrival of invasive plants can cause drastic changes to ecosystems, such as the displacement of native plant communities and the disruption of ecological functions. Ligustrum lucidum W.T. Aiton is an invasive tree species that has been registered in numerous regions worldwide. We analysed the effect of the expansion of L. lucidum on the edaphic properties and mycorrhizal fungal communities in forests of Celtis tala Gillies ex Planch. located in central–western Argentina. Sampling sites were established along a gradient of invasion, in which we measured the forest structure and soil physicochemical factors and identified the fungal species using morphological techniques. The analysis of the variance revealed severe changes in the tree structure and a decrease in the concentrations of organic matter and nitrogen in the invaded sites. Thirty-two Glomeromycota species were identified, belonging to six families. The abundance of Dentiscutata cerradensis decreased with the invasion, whereas Funneliformis mosseae and Septoglomus constrictum increased. The alpha diversity of the arbuscular mycorrhizal communities showed no differences between sites. The beta diversity decreased at invaded sites, indicating a tendency towards convergence and reduced variability in these communities in the presence of the exotic species.
Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations
Authors: Bernetti Mattia , Bussi Giovanni 
Published: September 2021

Abstract
Small-angle X-ray scattering (SAXS) experiments are arising as an effective instrument in the structural characterization of biomolecules in solution. However, they suffer from limited resolution, and complementing them with molecular dynamics (MD) simulations can be a successful strategy to obtain information at a finer scale. To this end, tools that allow computing SAXS spectra from MD-sampled structures have been designed over the years, mainly differing in how the solvent contribution is accounted for. In this context, RNA molecules represent a particularly challenging case, as they can have a remarkable effect on the surrounding solvent. Herein, we provide a comparison of SAXS spectra computed through different available software packages for a prototypical RNA system. RNA conformational dynamics is intentionally neglected so as to focus on solvent effects. The results highlight that solvent effects are important also at relatively low scattering vector, suggesting that approaches explicitly modeling solvent contribution are advisable when comparing with experimental data, while more efficient implicit-solvent methods can be a better choice as reaction coordinates to improve MD sampling on-the-fly.

Graphic abstract
Evaluation of an alternative biotreatment for the extraction of harmful iron and sulfur species from waterlogged wood
Authors: Monachon Mathilde , Albelda-Berenguer Magdalena , Lombardo Tiziana , Cornet Emilie , Moll-Dau Friederike , Schramm Janet , Schmidt-Ott Katharina , Joseph Edith 
Published: September 2021

AbstractAn innovative bioextraction method was tested and compared to common chemical extraction for the preservation of waterlogged archeological wood (WAW) artifacts. During burial, WAW artifacts accumulate iron and sulfur species forming iron sulfides. These compounds are harmless in the burial environment, where the oxygen content is low. But upon excavation, the WAW undergoes the oxidation of these compounds, and thus, irreversible physical and chemical damages occur. Fresh and archeological oak and pine samples were selected as representative species of WAW artifacts. Fresh samples were previously artificially contaminated to ascertain the presence of iron and sulfur. Thiobacillus denitrificans and natural iron chelators, called siderophores, were investigated to extract iron and sulfur as a 2-step biological treatment (BT) and compared to sodium persulfate–EDTA as chemical treatment (CT). Consolidation and freeze-drying were performed on the samples after BT and CT as traditional conservation protocols. BT and CT efficiency was evaluated through Raman, inductively coupled plasma–optical emission (ICP-OES), and Fourier transformed infrared (FTIR) spectroscopies. Raman and ICP showed that most of the iron and sulfur was extracted after BT, while some sulfur species remained present on CT samples. None of the extraction methods resulted in a degradation of the wood, as ascertained by FTIR analyses. Yet, all samples presented visual modifications after conservation. Pine samples treated with BT illustrated the oxidation of the species. Present principal component analysis (PCA) and analysis of variance (ANOVA) which were selected as statistical approaches and validated BT as a promising alternative extraction method, with encouraging extraction rates and less alteration of the sample appearance.
Tephra layers in the marine environment: a review of properties and emplacement processes
Authors: Freundt Armin , Schindlbeck-Belo Julie C. , Kutterolf Steffen , Hopkins Jenni L. 
Published: September 2021

Abstract
This review focuses on the recognition of volcanic ash occurrences in marine sediment cores and on using their appearance and properties to deduce their origin. Widespread marine tephra layers are important marker horizons for both volcanological as well as general geological investigations. We describe ash detection by visual inspection and logging of sediment cores. Ash layer structure and texture, particle morphologies and lithological compositions of primary volcanic deposits are summarized and processes modifying them are discussed, both natural processes acting on and in the seafloor, i.e. erosion and bioturbation, and anthropogenic modifications during drilling/coring and core preparation. We discuss primary emplacement processes of marine fall and flow tephra deposits derived from either subaerial or submarine sources in order to identify distinguishing properties. We also elaborate on processes generating secondary, resedimented volcaniclastic layers such as submarine landslides and shelf erosion as well as fluvial input and ice-rafting, and how they can be distinguished from primary volcaniclastic deposits, which is essential in tephrostratigraphy. Finally, methods of tephra correlation between cores and on-land deposits/volcanoes are illustrated because they allow us to extend the 1D information from single cores to 3D distribution and facies changes of tephras and to bridge the land–sea gap.
Optimal COVID-19 Vaccination Strategies with Limited Vaccine and Delivery Capabilities
Authors: Santini Simone 
Published: September 2021

We develop a model of infection spread that takes into account the existence of a vulnerable group as well as the variability of the social relations of individuals. We develop a compartmentalized power-law model, with power-law connections between the vulnerable and the general population, considering these connections as well as the connections among the vulnerable as parameters that we vary in our tests.
We use the model to study a number of vaccination strategies under two hypotheses: first, we assume a limited availability of vaccine but an infinite vaccination capacity, so all the available doses can be administered in a short time (negligible with respect to the evolution of the epidemic). Then, we assume a limited vaccination capacity, so the doses are administered in a time non-negligible with respect to the evolution of the epidemic.
We develop optimal strategies for the various social parameters, where a strategy consists of (1) the fraction of vaccine that is administered to the vulnerable population and (2) the criterion that is used to administer it to the general population. In the case of a limited vaccination capacity, the fraction (1) is a function of time, and we study how to optimize it to obtain a maximal reduction in the number of fatalities.