bluuebunny/crossref_metadata_2025 huggingface dataset:
Combined atrial fibrillation ablation and left atrial appendage occlusion procedure in the United States: a propensity score matched analysis from 2016–2019 national readmission database
Authors: Pasupula Deepak Kumar , Siddappa Malleshappa Sudeep K , Munir Muhammad B , Bhat Anusha Ganapati , Anandaraj Antony , Jakkoju Avaneesh , Spooner Michael , Koranne Ketan , Hsu Jonathan C , Olshansky Brian , Camm A John
Published: November 2022

Aims

The safety and feasibility of combining percutaneous catheter ablation (CA) for atrial fibrillation with left atrial appendage occlusion (LAAO) as a single procedure in the USA have not been investigated. We analyzed the US National Readmission Database (NRD) to investigate the incidence of combined LAAO + CA and compare major adverse cardiovascular events (MACEs) with matched LAAO-only and CA-only patients.

Methods and results

In this retrospective study from NRD data, we identified patients undergoing combined LAAO and CA procedures on the same day in the USA from 2016 to 2019. A 1:1 propensity score match was performed to identify patients undergoing LAAO-only and CA-only procedures. The number of LAAO + CA procedures increased from 28 (2016) to 119 (2019). LAAO + CA patients (n = 375, mean age 74 ± 9.2 years, 53.4% were males) had non-significant higher MACE (8.1%) when compared with LAAO-only (n = 407, 5.3%) or CA-only patients (n = 406, 7.4%), which was primarily driven by higher rate of pericardial effusion (4.3%). All-cause 30-day readmission rates among LAAO + CA patients (10.7%) were similar when compared with LAAO-only (12.7%) or CA-only (17.5%) patients. The most frequent primary reason for readmissions among LAAO + CA and LAAO-only cohorts was heart failure (24.6 and 31.5%, respectively), while among the CA-only cohort, it was paroxysmal atrial fibrillation (25.7%).

Conclusion

We report an 63% annual growth (from 28 procedures) in combined LAAO and CA procedures in the USA. There were no significant difference in MACE and all-cause 30-day readmission rates among LAAO + CA patients compared with matched LAAO-only or CA-only patients.
Atrial fibrillation onset before heart failure or vice versa: what is worst? A nationwide register study
Authors: Pallisgaard Jannik , Greve Anders M , Lock-Hansen Morten , Thune Jens Jakob , Fosboel Emil Loldrup , Devereux Richard B , Okin Peter M , Gislason Gunnar H , Torp-Pedersen Christian , Bang Casper N
Published: November 2022

Aims

Atrial fibrillation (AF) and heart failure (HF) often coexist. However, whether AF onset before HF or vice versa is associated with the worst outcome remains unclear. A consensus of large studies can guide future research and preventive strategies to better target high-risk patients.

Methods and results

We included all Danish cases with the coexistence of AF and HF (2005–17) using nationwide registries. Patients were divided into three separate groups (i) AF before HF, (ii) HF before AF, or (iii) AF and HF diagnosed concurrently (±30 days). Adjusting landmark Cox analyses (index date was the time of the latter diagnosis of AF or HF) were used for evaluating the association of the three groups with a composite outcome of ischaemic stroke or death. Among a total of 49 042 patients included, 40% had AF before HF, 27% had HF before AF, and 33% had AF and HF diagnosed concurrently. The composite endpoint accrued more often in patients with HF before AF compared to the two other groups (<0.001), and this remained significant in the adjusted analyses with hazard ratios (95% confidence intervals) of 1.26 (1.22–1.30) compared to AF before HF. Finally, antihypertensive treatment, oral anticoagulants, amiodarone, statins, and AF ablation were associated with a lower hazard ratio of the composite endpoint (all < 0.001).

Conclusions

In this large Danish national cohort, diagnosis of HF before AF was associated with an increased absolute risk of death compared to AF before HF and AF and HF diagnosed concurrently. Antihypertensive treatment, oral anticoagulants, amiodarone, statins, and AF ablation may improve prognosis.
Quantitative assessment of transmural fibrosis profile in the human atrium: evidence for a three-dimensional arrhythmic substrate by slice-to-slice histology
Authors: Ravelli Flavia , Masè Michela , Cristoforetti Alessandro , Avogaro Laura , D’Amato Elvira , Tessarolo Francesco , Piccoli Federico , Graffigna Angelo
Published: November 2022

Aims

Intramural fibrosis represents a crucial factor in the formation of a three-dimensional (3D) substrate for atrial fibrillation (AF). However, the transmural distribution of fibrosis and its relationship with atrial overload remain largely unknown. The aim of this study is to quantify the transmural profile of atrial fibrosis in patients with different degrees of atrial dilatation and arrhythmic profiles by a high-resolution 3D histology method.

Methods and results

Serial microtome-cut tissue slices, sampling the entire atrial wall thickness at 5 µm spatial resolution, were obtained from right atrial appendage specimens in 23 cardiac surgery patients. Atrial slices were picrosirius red stained, imaged by polarized light microscopy, and analysed by a custom-made segmentation algorithm. In all patients, the intramural fibrosis content displayed a progressive decrease alongside tissue depth, passing from 68.6 ± 11.6% in the subepicardium to 10–13% in the subendocardium. Distinct transmural fibrotic profiles were observed in patients with atrial dilatation with respect to control patients, where the first showed a slower decrease of fibrosis along tissue depth (exponential decay constant: 171.2 ± 54.5 vs. 80.9 ± 24.4 µm, P < 0.005). Similar slow fibrotic profiles were observed in patients with AF (142.8 ± 41.7 µm). Subepicardial and midwall levels of fibrosis correlated with the degree of atrial dilatation (ρ = 0.72, P < 0.001), while no correlation was found in subendocardial layers.

Conclusions

Quantification of fibrosis transmural profile at high resolution is feasible by slice-to-slice histology. Deeper penetration of fibrosis in subepicardial and midwall layers in dilated atria may concur to the formation of a 3D arrhythmic substrate.
The bacteriome of the halophyte Atriplex nummularia (old man saltbush) in salt-affected soils - an ecological model
Authors: Alfradique Monteiro Douglas , Fazolato Carolline Silva Barbosa , Martins Luiz Fernando , Tavora Coelho da Costa Rachid Caio
Published: November 2022

Halophytes, plants capable of growing under saline conditions, are an important source of bacteria with biotechnological potential for plant growth under extreme conditions. In this study, we evaluated the halophyte Atriplex nummularia bacteriome assemblage from three different salinized sites in northeastern Brazil with different edaphoclimatic characteristics, understanding the participation of the plant in the assembly of its microbiome. We sampled 30 specimens, from which the leaves, roots, and rhizospheric soil were subjected to 16S rRNA gene sequencing, bringing forth patterns of alpha and beta diversity, taxonomical composition, co-occurrence network, and the core microbiome of each compartment. Overall, this species harbors a very restricted set of endophytic microbes, and communities showed an increasing gradient of complexity (soil > root > leaf), reflecting a change in the main selective pressure being active over the microbial community. Although the leaf bacteriome was influenced basically by host factors, the soil community was modulated by the environment, and the root bacteriome was structured by both factors. These results help us understand how plant–microbe interactions occur in saline environments. As these plants shelter microbes that potentially alleviate abiotic stresses, we discuss how culture-independent methods could contribute to the prospection of plant growth promoting bacteria in plants.
Prepandemic Social Integration: Protection or Risk for Older Adults in the Time of COVID-19?
Authors: Li Lydia W , Hu Rita Xiaochen , Luo Meng Sha , McLaughlin Sara J
Published: November 2022

Objectives

To examine the association between prepandemic social integration and posttraumatic stress disorder (PTSD) symptoms during the coronavirus disease 2019 (COVID-19) pandemic and test whether the association is mediated by social support received and social events missed during the pandemic. We also explored age, race, gender, and socioeconomic differences in the association.

Methods

We adopted a prospective design. Path analysis was conducted using data from the COVID-19 supplement (2020) and the 2019 wave of the National Health and Aging Trends Study (NHATS). The sample represents Medicare beneficiaries aged 70 years and older (N = 2,694). Social integration was measured using a six-item index. A standardized scale assessed PTSD symptoms. Both social support received and social events missed were single-item measures. The analysis controlled for sociodemographic characteristics, prepandemic physical and mental health, and coronavirus exposure during the pandemic.

Results

Prepandemic social integration was positively associated with PTSD symptoms during the pandemic. The association was primarily mediated by social events missed—high levels of prepandemic social integration were associated with missing more social events during the pandemic resulting in more PTSD symptoms. Social support received was also a mediator—social integration was positively associated with social support received during the pandemic, with more received support associated with greater PTSD symptoms. Prepandemic social integration had no significant direct effect on PTSD symptoms. The direct, indirect, and total effects of social integration on PTSD symptoms did not significantly differ by age, race, gender, education, or poverty status.

Discussion

Social integration may carry mental health risks in times of infectious disease outbreaks.
Empirical correlations between an FAS non-ergodic ground motion model and a GIT derived model for Central Italy
Authors: Morasca P , D'Amico M , Sgobba S , Lanzano G , Colavitti L , Pacor F , Spallarossa D
Published: November 2022

In this study, we investigate the correlation between the residuals of a neGMM (non-ergodic Ground Motion Model) and the physics-based parameters obtained using a non-parametric GIT approach (Generalized Inversion Technique) to lay the groundwork for the implementation of an ad-hoc FAS (Fourier Amplitude Spectra) neGMM for the Central Italy region. This region is particularly suitable for data-driven methodologies as those applied in this work because of the large amount of available data due to the recent multiple main shock–aftershock sequences occurred in this area. Both neGMM and GIT models are developed for Fourier spectra in the frequency range between 0.5 and 25 Hz and using the same reference sites. The comparison of the non-ergodic terms with the source, path and site spectral parameters provides interesting results. First, we find a strong correlation between the source parameters, stress drop Δσ and decay ${k}_{\mathrm{ source}}$ and the source neGMM corrective terms (the combination of the between-event δBe and the location-to-location terms δL2L). This correlation is frequency dependent and, at high frequency, is remarkably positive for Δσ and negative for ${k}_{\mathrm{ source}}$. Concerning the attenuation terms, the path-to-path residuals (δP2P) are clearly associated with the deviations from the regional Q estimates obtained from GIT analysis. This indicates that the neGMM properly captures the properties of the anelastic attenuation and that the corrective terms δP2P can be used to account for differences in travel paths across different crustal domains. Finally, adopting the same reference sites for neGMM and non-parametric GIT, we observe that the systematic site terms (δS2Ss) and the GIT-derived amplification functions are in good agreement. The next step for an appropriate modelling is to identify the physical parameters (e.g. VS,30 and ${k}_0$) describing the empirical amplification curves to be introduced as explanatory variables in the ground motion model.
The Modified Mucosal Inflammation Noninvasive Index and Endoscopic Remission in Adults With Crohn’s Disease
Authors: Yogev Dotan , Verstockt Bram , Dignass Axel , Focht Gili , Atia Ohad , Dotan Iris , Vermeire Severine , Turner Dan
Published: November 2022

Lay Summary

The Mucosal Inflammation Noninvasive Index is a validated noninvasive tool to assess endoscopic remission in pediatric Crohn’s disease. In this study, we evaluated a modified version of the Mucosal Inflammation Noninvasive Index on adult cohorts to explore its validly in adult Crohn’s disease.
Maternal age and the risk of low birthweight and pre-term delivery: a pan-Nordic comparison
Authors: Aradhya Siddartha , Tegunimataka Anna , Kravdal Øystein , Martikainen Pekka , Myrskylä Mikko , Barclay Kieron , Goisis Alice
Published: November 2022

Background

Advanced maternal age at birth is considered a risk factor for adverse birth outcomes. A recent study applying a sibling design has shown, however, that the association might be confounded by unobserved maternal characteristics.

Methods

Using total population register data on all live singleton births during the period 1999–2012 in Denmark (N = 580 133; 90% population coverage), Norway (N = 540 890) and Sweden (N = 941 403) and from 2001–2014 in Finland (N = 568 026), we test whether advanced maternal age at birth independently increases the risk of low birthweight (LBW) (<2500 g) and pre-term birth (<37 weeks gestation). We estimated within-family models to reduce confounding by unobserved maternal characteristics shared by siblings using three model specifications: Model 0 examines the bivariate association; Model 1 adjusts for parity and sex; Model 2 for parity, sex and birth year.

Results

The main results (Model 1) show an increased risk in LBW and pre-term delivery with increasing maternal ages. For example, compared with maternal ages of 26–27 years, maternal ages of 38–39 years display a 2.2, 0.9, 2.1 and 2.4 percentage point increase in the risk of LBW in Denmark, Finland, Norway and Sweden, respectively. The same patterns hold for pre-term delivery.

Conclusions

Advanced maternal age is independently associated with higher risk of poor perinatal health outcomes even after adjusting for all observed and unobserved factors shared between siblings.
Comparing single-sitting versus modular text message surveys in Egypt
Authors: Haas Georg-Christoph , Keusch Florian , Frölich Markus
Published: November 2022

Text message surveys enable cost-efficient data collection and can be applied with hard-to-reach populations while other survey modes suffer from undercoverage in regions with low landline and/or internet penetration. Little is known about how to best administer surveys in this mode. We experimentally compared two different designs of automated text message surveys in terms of response rate, nonresponse bias, and participation in a follow-up survey in Egypt. In the single-sitting design, respondents automatically received a text message with a new question once they replied to a question. In the modular design, respondents received a new question each day, regardless of whether they had responded to the previous question. We invited 1,081 Egyptian parents of kindergarten children who owned a mobile phone to participate in a text message survey with eight questions on the nutrition behavior of their children. We found that, compared to the single-sitting design, the modular design yielded a higher number of answered questions but had fewer fully completed questionnaires. We found no nonresponse bias in either group and no difference in the probability of responding to a follow-up survey. Our results will help researchers make design decisions about how to implement text message surveys.
A test of the “hybridity hypothesis:” support for celebrity political expression, political ideology, and need for cognitive closure
Authors: Young Dannagal G , Oittinen Erin , Hoffman Lindsay H , Lambe Jennifer L
Published: November 2022

Are conservatives more likely than liberals to oppose celebrity political expression? And if so, is this attributable to the overwhelmingly liberal ideology of the actors, musicians, and athletes who speak out on political matters? The hybridity hypothesis suggests that opposition to celebrity political expression might also be grounded in individuals’ psychological predispositions and resulting aesthetic preferences. Using 2018 national CCES data (N = 1000), we test the relationships between political beliefs, psychological traits, and support for celebrity political expression. Results indicate that need for cognitive closure is significantly negatively associated with support for celebrity expression, and that this relationship functions independently of the political leanings of the audience and of the political nature of the expression being made. The notion that a psychological need for closure is associated with less approval of certain forms of political discourse has important democratic implications, especially given the documented link between need for cognitive closure and political conservatism.
A consensus building study to define the role of a ‘clinical’ pharmacy technician in a Primary Care Network environment in England
Authors: Street Kerry A , Taylor Andrea D J
Published: November 2022

Objective

To define criteria of the role of a clinical pharmacy technician that can be applied to the Primary Care Network environment in England.

Method

Consensus building study using Delphi methodology conducted in three stages: Stage 1: topic generation from a literature review; Stage 2: Delphi process via Jisc Online Surveys; Stage 3: analysis and presentation of identiﬁed topics.

Key findings

A consensus-defined list of 61 criteria appropriate for the role description of a clinical pharmacy technician across all healthcare sectors was derived. This was refined to 35 criteria considered most important to the role of a clinical pharmacy technician working in a Primary Care Network environment. A qualitative analysis of expert panel comments identified the importance of defining the level at which a pharmacy technician conducts each element of the role, suggesting they would be working at an ‘advanced’ level. Due to the advanced nature of this role, day-to-day supervision would be less than that of a pharmacy technician, and usually conducted by a pharmacist. This research supports existing international literature that a clinical pharmacy technician role releases capacity for other healthcare professionals to focus on more complex patient cases.

Conclusion

This research has provided a defined list of criteria considered appropriate for the role description of a clinical pharmacy technician. The need to evidence levels of pharmacy technician practice against recognised competency frameworks alongside clear role descriptors was noted. This study adds to the limited international research about pharmacy technician roles and supports the International Pharmaceutical Federation Pharmaceutical workforce development goals.
Recursive moment computation in Filon methods and application to high-frequency wave scattering in two dimensions
Authors: Maierhofer G , Iserles A , Peake N
Published: November 2022

We study the efficient approximation of highly oscillatory integrals using Filon methods. A crucial step in the implementation of these methods is the accurate and fast computation of the Filon quadrature moments. In this work we demonstrate how recurrences can be constructed for a wide class of oscillatory kernel functions, based on the observation that many physically relevant kernel functions are in the null space of a linear differential operator whose action on the Filon interpolation basis is represented by a banded (infinite) matrix. We discuss in further detail the application to two classes of particular interest: integrals with algebraic singularities and stationary points and integrals involving a Hankel function. We provide rigorous stability results for the moment computation for the first of these classes and demonstrate how the corresponding Filon method results in an accurate approximation at truly frequency-independent cost. For the Hankel kernel, we derive error estimates that describe the convergence behaviour of the method in terms of frequency and number of Filon quadrature points. Finally, we show how Filon methods with recursive moment computation can be applied to efficiently compute integrals arising in hybrid numerical-asymptotic collocation methods for high-frequency wave scattering on a screen.
Household Transmission Dynamics of Seasonal Human Coronaviruses
Authors: Quandelacy Talia M , Hitchings Matt D T , Lessler Justin , Read Jonathan M , Vukotich Charles , Azman Andrew S , Salje Henrik , Zimmer Shanta , Gao Hongjiang , Zheteyeva Yenlik , Uzicanin Amra , Cummings Derek A T
Published: November 2022

Background

Household transmission studies inform how viruses spread among close contacts, but few characterize household transmission of endemic coronaviruses.

Methods

We used data collected from 223 households with school-age children participating in weekly disease surveillance over 2 respiratory virus seasons (December 2015 to May 2017), to describe clinical characteristics of endemic human coronaviruses (HCoV-229E, HcoV-HKU1, HcoV-NL63, HcoV-OC43) infections, and community and household transmission probabilities using a chain-binomial model correcting for missing data from untested households.

Results

Among 947 participants in 223 households, we observed 121 infections during the study, most commonly subtype HCoV-OC43. Higher proportions of infected children (<19 years) displayed influenza-like illness symptoms than infected adults (relative risk, 3.0; 95% credible interval [CrI], 1.5–6.9). The estimated weekly household transmission probability was 9% (95% CrI, 6–13) and weekly community acquisition probability was 7% (95% CrI, 5–10). We found no evidence for differences in community or household transmission probabilities by age or symptom status. Simulations suggest that our study was underpowered to detect such differences.

Conclusions

Our study highlights the need for large household studies to inform household transmission, the challenges in estimating household transmission probabilities from asymptomatic individuals, and implications for controlling endemic CoVs.
Automatic crack classification and segmentation on concrete bridge images using convolutional neural networks and hybrid image processing
Authors: Li Baoxian , Guo Hongbin , Wang Zhanfei , Li Mingyang
Published: November 2022

Cracks are an indicator for a bridge’s structural health and functional failures. Crack detection is one of the major tasks needed to maintain the structural health and serviceability of a bridge. At present, the most commonly used crack detection technology is manual inspection, which has the disadvantages of being highly labor-intensive and time-consuming. In this paper, a crack detection method based on a convolutional neural network (CNN) is proposed. To automate quantitative measurements of an identified crack, hybrid image processing is proposed, as well. First, a dataset is compiled, including 12,000 cropped crack images and 19,500 cropped background images. Second, preprocessed images with the proposed method of Bilateral-Graying-Contrast (BGC) are fed into ResNet and a Visual Geometry Group Network (VGG) for training and testing. Finally, an automatic measurement system for bridge crack is developed which is not prone to weakened shooting conditions. The results demonstrate that ResNet achieves an accuracy of crack detection up to 97.44%, which is higher than VGG. Our crack measurement system significantly reduces the measurement error to 9.86% and can be assumed as a reliable method in the analysis of concrete bridge images.
Are richer neighborhoods always better for the kids?
Authors: Markussen Simen , Røed Knut
Published: November 2022

Based on Norwegian administrative registers, we provide new empirical evidence on the effects of the childhood neighborhood’s socioeconomic status on early educational performance. A neighborhood’s status is measured annually by its adult inhabitants’ earnings ranks within larger commuting zones, and the childhood neighborhood status is the average status of the neighborhoods inhabited from the year after birth to age 15. Identification of causal effects relies on within-family comparisons only. Our results reveal a distinct hump-shaped relationship between the socioeconomic status of the childhood neighborhood and school results at age 15–16, such that the optimal neighborhood is of medium rank.
The growth and metabolome of Saccharomyces uvarum in wine fermentations are strongly influenced by the route of nitrogen assimilation
Authors: Coral-Medina Angela , Morrissey John P , Camarasa Carole
Published: November 2022

Nitrogen is a critical nutrient in beverage fermentations, influencing fermentation performance and formation of compounds that affect organoleptic properties of the product. Traditionally, most commercial wine fermentations rely on Saccharomyces cerevisiae but the potential of alternative yeasts is increasingly recognised because of the possibility to deliver innovative products and process improvements. In this regard, Saccharomyces uvarum is an attractive non-traditional yeast that, while quite closely related to S. cerevisiae, displays a different fermentative and aromatic profile. Although S. uvarum is used in cider-making and in some winemaking, better knowledge of its physiology and metabolism is required if its full potential is to be realised. To address this gap, we performed a comparative analysis of the response of S. uvarum and S. cerevisiae to 13 different sources of nitrogen, assessing key parameters such as growth, fermentation performance, the production of central carbon metabolites and aroma volatile compounds. We observed that the two species differ in the production of acetate, succinate, medium-chain fatty acids, phenylethanol, phenylethyl acetate, and fusel/branched acids in ways that reflect different distribution of fluxes in the metabolic network. The integrated analysis revealed different patterns of yeast performance and activity linked to whether growth was on amino acids metabolised via the Ehrlich pathway or on amino acids and compounds assimilated through the central nitrogen core. This study highlights differences between the two yeasts and the importance that nitrogen metabolism can play in modulating the sensory profile of wine when using S. uvarum as the fermentative yeast.
Ecology of large felids and their prey in small reserves of the Yucatán Peninsula of Mexico
Authors: Piña-Covarrubias Evelyn , Chávez Cuauhtémoc , Chapman Mark A , Morales Montserrat , Elizalde-Arellano Cynthia , Doncaster C Patrick
Published: November 2022

Jaguars and pumas are top-predator species in the Neotropics that are threatened by habitat destruction, illegal poaching of their body parts and their favored prey, and by the human–wildlife conflicts that arise when predators attack livestock. Much of the remaining felid habitat in the Americas is in protected nature reserves that are too small and isolated to support local populations. Surrounding forests therefore play a vital role in felid conservation. Successful long-term conservation of these two felids requires evidence-based knowledge of their biological and ecological requirements. We studied population distributions of jaguars and pumas and their prey in and between two small, private reserves of the Northern Yucatán Peninsula, Mexico, with areas of 25 and 43 km2. During 2 years of camera trapping (2015 and 2016), we detected 21 jaguars, from which we estimated an average space requirement of 28–45 km2/individual. Dietary niche overlap exceeded random expectation. The most frequently occurring prey items in jaguar and puma diets were collared peccary and deer. Jaguar also favored nine-banded armadillos and white-nosed coati, while puma favored canids. Both felids avoided ocellated turkey. Overall, diet of jaguars was less species-rich, but similar in niche breadth, to that of pumas. A fluid use of space by both species, in 2015 tending toward mutual attraction and in 2016 toward partial exclusion of pumas by jaguars, combined with the high dietary overlap, is consistent with a dominance hierarchy facilitating coexistence. Jaguars and pumas favor the same prey as the people in local communities who hunt, which likely will intensify human–wildlife impacts when prey become scarce. We conclude that even small reserves play an important role in increasing the continuity of habitat for prey and large felids, whose generalist habits suppress interspecific competition for increasingly limiting prey that are largely shared between them and humans.
Wenlin procedure combined with Wung procedure for treatment of severe pectus carinatum
Authors: Wang Wenlin , Long Weiguang , Liu Yang , Cai Bin , Luo Juan
Published: November 2022

Pectus carinatum can be treated with a single minimally invasive surgery, but the severe cases will appear secondary depression after treatment, which needs to be corrected additionally. We used the combined Wenlin procedure and Wung procedure to treat a patient with severe pectus carinatum and achieved satisfactory results.
COVID-19 Vaccination in a Military Population: Evaluation of a Quality Improvement Initiative to Increase Vaccine Confidence and Reduce Hesitancy
Authors: Batie Carolyn M , Hintz Courtney N , Catchings Susan H , Thompson Julie A , Sabol Valerie K
Published: November 2022

Introduction

Extensive efforts have been directed toward developing an effective vaccine to fight against the Coronavirus Disease 2019 (COVID-19); however, hesitancy to receive COVID-19 vaccinations has become detrimental to overcoming the COVID-19 pandemic. Although the U.S. Military instated a COVID-19 vaccine mandate, some members were still hesitant to receive the vaccine. To determine the efficacy of a program focused on vaccine hesitation, a program evaluation was conducted on a COVID-19 vaccine educational intervention (hereafter COVID-19 Educational Presentation) for trainees at Lackland Air Force Base, TX, in September 2021. Objectives of the educational session included (1) determining the participants’ level of confidence that the COVID-19 vaccines are safe and effective, (2) understanding the concern for long-term side effects from COVID-19 vaccinations, and (3) identifying the driving forces behind hesitancy to receive a COVID-19 vaccination.

Materials and Methods

We reviewed data collected from the COVID-19 Vaccine Educational Presentation; it consisted of a PowerPoint presentation addressing common questions and myths about COVID-19 vaccines. A survey instrument called the COVID-19 Hesitancy and Confidence Survey was created to assess attitudes to receive the COVID-19 vaccine

Results

Two voluntary COVID-19 Educational Presentations were given in September 2, 2021, months prior to the Air Force’s COVID-19 vaccine mandate deadline; 128 trainees participated in the assessment surveys. Overall, the educational intervention increased confidence to receive the COVID-19 vaccine increased by 12.6% (t = −7.928, P < 0.001).

Conclusions

The COVID-19 Educational Presentation increased confidence and decreased hesitancy to receive the COVID-19 vaccine. Vaccine educational programs should continue in the military population to help combat misinformation and ensure that our military force is fully vaccinated and able to maintain mission readiness.
Motivations for a large self-interacting dark matter cross-section from Milky Way satellites
Authors: Silverman Maya , Bullock James S , Kaplinghat Manoj , Robles Victor H , Valli Mauro
Published: November 2022

We explore the properties of Milky Way (MW) subhaloes in self-interacting dark matter models for moderate cross-sections of 1–5 cm2 g−1 using high-resolution zoom-in N-body simulations. We include the gravitational potential of a baryonic disc and bulge matched to the MW, which is critical for getting accurate predictions. The predicted number and distribution of subhaloes within the host halo are similar for 1 and 5 cm2 g−1 models, and they agree with observations of MW satellite galaxies only if subhaloes with peak circular velocity over all time >7 km s−1 are able to form galaxies. We do not find distinctive signatures in the pericentre distribution of the subhaloes that could help distinguish the models. Using an analytical model to extend the simulation results, we are able to show that subhaloes in models with cross-sections between 1 and 5 cm2 g−1 are not dense enough to match the densest ultrafaint and classical dwarf spheroidal galaxies in the MW. This motivates exploring velocity-dependent cross-sections with values larger than 5 cm2 g−1 at the velocities relevant for the satellites such that core collapse would occur in some of the ultrafaint and classical dwarf spheroidals.
Using peculiar velocity surveys to constrain the growth rate of structure with the wide-angle effect
Authors: Lai Yan , Howlett Cullan , Davis Tamara M
Published: November 2022

Amongst the most popular explanations for dark energy are modified theories of gravity. The galaxy overdensity and peculiar velocity fields help us to constrain the growth rate of structure and distinguish different models of gravity. We introduce an improved method for constraining the growth rate of structure with the galaxy overdensity and peculiar velocity fields. This method reduces the modelling systematic error by accounting for the wide-angle effect and the zero-point calibration uncertainty during the modelling process. We also speed up the posterior sampling by around 30 times by first calculating the likelihood at a small number of fiducial points and then interpolating the likelihood values during MCMC sampling. We test the new method on mocks and we find it is able to recover the fiducial growth rate of structure. We applied our new method to the SDSS PV catalogue, which is the largest single peculiar velocity catalogue to date. Our constraint on the growth rate of structure is $f\sigma _8 = 0.405_{-0.071}^{+0.076}$ (stat) ±0.009 (sys) at the effective redshift of 0.073. Our constraint is consistent with a Planck 2018 cosmological model, fσ8 = 0.448, within one standard deviation. Our improved methodology will enable similar analysis on future data, with even larger sample sizes and covering larger angular areas on the sky.
LitCovid in 2022: an information resource for the COVID-19 literature
Authors: Chen Qingyu , Allot Alexis , Leaman Robert , Wei Chih-Hsuan , Aghaarabi Elaheh , Guerrerio John J , Xu Lilly , Lu Zhiyong
Published: November 2022

LitCovid (https://www.ncbi.nlm.nih.gov/research/coronavirus/)—first launched in February 2020—is a first-of-its-kind literature hub for tracking up-to-date published research on COVID-19. The number of articles in LitCovid has increased from 55 000 to ∼300 000 over the past 2.5 years, with a consistent growth rate of ∼10 000 articles per month. In addition to the rapid literature growth, the COVID-19 pandemic has evolved dramatically. For instance, the Omicron variant has now accounted for over 98% of new infections in the United States. In response to the continuing evolution of the COVID-19 pandemic, this article describes significant updates to LitCovid over the last 2 years. First, we introduced the long Covid collection consisting of the articles on COVID-19 survivors experiencing ongoing multisystemic symptoms, including respiratory issues, cardiovascular disease, cognitive impairment, and profound fatigue. Second, we provided new annotations on the latest COVID-19 strains and vaccines mentioned in the literature. Third, we improved several existing features with more accurate machine learning algorithms for annotating topics and classifying articles relevant to COVID-19. LitCovid has been widely used with millions of accesses by users worldwide on various information needs and continues to play a critical role in collecting, curating and standardizing the latest knowledge on the COVID-19 literature.
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource
Authors: Sollis Elliot , Mosaku Abayomi , Abid Ala , Buniello Annalisa , Cerezo Maria , Gil Laurent , Groza Tudor , Güneş Osman , Hall Peggy , Hayhurst James , Ibrahim Arwa , Ji Yue , John Sajo , Lewis Elizabeth , MacArthur Jacqueline A L , McMahon Aoife , Osumi-Sutherland David , Panoutsopoulou Kalliope , Pendlington Zoë , Ramachandran Santhi , Stefancsik Ray , Stewart Jonathan , Whetzel Patricia , Wilson Robert , Hindorff Lucia , Cunningham Fiona , Lambert Samuel A , Inouye Michael , Parkinson Helen , Harris Laura W
Published: November 2022

The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.
GenBank 2023 update
Authors: Sayers Eric W , Cavanaugh Mark , Clark Karen , Pruitt Kim D , Sherry Stephen T , Yankie Linda , Karsch-Mizrachi Ilene
Published: November 2022

GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 19.6 trillion base pairs from over 2.9 billion nucleotide sequences for 504 000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. Recent updates include resources for data from the SARS-CoV-2 virus, NCBI Datasets, BLAST ClusteredNR, the Submission Portal, table2asn, a Foreign Contamination Screening tool and BioSample.
Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis
Authors: Rietmeyer Lauriane , Li De La Sierra-Gallay Inès , Schepers Guy , Dorchêne Delphine , Iannazzo Laura , Patin Delphine , Touzé Thierry , van Tilbeurgh Herman , Herdewijn Piet , Ethève-Quelquejeu Mélanie , Fonvielle Matthieu
Published: November 2022

Xenobiotic nucleic acids (XNAs) offer tremendous potential for synthetic biology, biotechnology, and molecular medicine but their ability to mimic nucleic acids still needs to be explored. Here, to study the ability of XNA oligonucleotides to mimic tRNA, we synthesized three L-Ala-tXNAs analogs. These molecules were used in a non-ribosomal peptide synthesis involving a bacterial Fem transferase. We compared the ability of this enzyme to use amino-acyl tXNAs containing 1′,5′-anhydrohexitol (HNA), 2′-fluoro ribose (2′F-RNA) and 2′-fluoro arabinose. L-Ala-tXNA containing HNA or 2′F-RNA were substrates of the Fem enzyme. The synthesis of peptidyl-XNA and the resolution of their structures in complex with the enzyme show the impact of the XNA on protein binding. For the first time we describe functional tXNA in an in vitro assay. These results invite to test tXNA also as substitute for tRNA in translation.
YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis
Authors: Teixeira Miguel Cacho , Viana Romeu , Palma Margarida , Oliveira Jorge , Galocha Mónica , Mota Marta Neves , Couceiro Diogo , Pereira Maria Galhardas , Antunes Miguel , Costa Inês V , Pais Pedro , Parada Carolina , Chaouiya Claudine , Sá-Correia Isabel , Monteiro Pedro Tiago
Published: November 2022

YEASTRACT+ (http://yeastract-plus.org/) is a tool for the analysis, prediction and modelling of transcription regulatory data at the gene and genomic levels in yeasts. It incorporates three integrated databases: YEASTRACT (http://yeastract-plus.org/yeastract/), PathoYeastract (http://yeastract-plus.org/pathoyeastract/) and NCYeastract (http://yeastract-plus.org/ncyeastract/), focused on Saccharomyces cerevisiae, pathogenic yeasts of the Candida genus, and non-conventional yeasts of biotechnological relevance. In this release, YEASTRACT+ offers upgraded information on transcription regulation for the ten previously incorporated yeast species, while extending the database to another pathogenic yeast, Candida auris. Since the last release of YEASTRACT+ (January 2020), a fourth database has been integrated. CommunityYeastract (http://yeastract-plus.org/community/) offers a platform for the creation, use, and future update of YEASTRACT-like databases for any yeast of the users’ choice. CommunityYeastract currently provides information for two Saccharomyces boulardii strains, Rhodotorula toruloides NP11 oleaginous yeast, and Schizosaccharomyces pombe 972h-. In addition, YEASTRACT+ portal currently gathers 304 547 documented regulatory associations between transcription factors (TF) and target genes and 480 DNA binding sites, considering 2771 TFs from 11 yeast species. A new set of tools, currently implemented for S. cerevisiae and C. albicans, is further offered, combining regulatory information with genome-scale metabolic models to provide predictions on the most promising transcription factors to be exploited in cell factory optimisation or to be used as novel drug targets. The expansion of these new tools to the remaining YEASTRACT+ species is ongoing.
scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes
Authors: Cha Junha , Yu Jiwon , Cho Jae-Won , Hemberg Martin , Lee Insuk
Published: November 2022

A major challenge in single-cell biology is identifying cell-type-specific gene functions, which may substantially improve precision medicine. Differential expression analysis of genes is a popular, yet insufficient approach, and complementary methods that associate function with cell type are required. Here, we describe scHumanNet (https://github.com/netbiolab/scHumanNet), a single-cell network analysis platform for resolving cellular heterogeneity across gene functions in humans. Based on cell-type-specific gene networks (CGNs) constructed under the guidance of the HumanNet reference interactome, scHumanNet displayed higher functional relevance to the cellular context than CGNs built by other methods on single-cell transcriptome data. Cellular deconvolution of gene signatures based on network compactness across cell types revealed breast cancer prognostic markers associated with T cells. scHumanNet could also prioritize genes associated with particular cell types using CGN centrality and identified the differential hubness of CGNs between disease and healthy conditions. We demonstrated the usefulness of scHumanNet by uncovering T-cell-specific functional effects of GITR, a prognostic gene for breast cancer, and functional defects in autism spectrum disorder genes specific for inhibitory neurons. These results suggest that scHumanNet will advance our understanding of cell-type specificity across human disease genes.
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome
Authors: Zhou Hufeng , Arapoglou Theodore , Li Xihao , Li Zilin , Zheng Xiuwen , Moore Jill , Asok Abhijith , Kumar Sushant , Blue Elizabeth E , Buyske Steven , Cox Nancy , Felsenfeld Adam , Gerstein Mark , Kenny Eimear , Li Bingshan , Matise Tara , Philippakis Anthony , Rehm Heidi L , Sofia Heidi J , Snyder Grace ,   NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Weng Zhiping , Neale Benjamin , Sunyaev Shamil R , Lin Xihong
Published: November 2022

Large biobank-scale whole genome sequencing (WGS) studies are rapidly identifying a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant functional annotations play a critical role in WGS analysis, result interpretation, and prioritization of disease- or trait-associated causal variants. Existing functional annotation databases have limited scope to perform online queries and functionally annotate the genotype data of large biobank-scale WGS studies. We develop the Functional Annotation of Variants Online Resources (FAVOR) to meet these pressing needs. FAVOR provides a comprehensive multi-faceted variant functional annotation online portal that summarizes and visualizes findings of all possible nine billion single nucleotide variants (SNVs) across the genome. It allows for rapid variant-, gene- and region-level queries of variant functional annotations. FAVOR integrates variant functional information from multiple sources to describe the functional characteristics of variants and facilitates prioritizing plausible causal variants influencing human phenotypes. Furthermore, we provide a scalable annotation tool, FAVORannotator, to functionally annotate large-scale WGS studies and efficiently store the genotype and their variant functional annotation data in a single file using the annotated Genomic Data Structure (aGDS) format, making downstream analysis more convenient. FAVOR and FAVORannotator are available at https://favor.genohub.org.
TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms
Authors: Zhou Ziheng , Tan Cong , Chau Matthew Hoi Kin , Jiang Xiaosen , Ke Ziyuan , Chen Xiaoyan , Cao Ye , Kwok Yvonne K , Bellgard Matthew , Leung Tak Yeung , Choy Kwong Wai , Dong Zirui
Published: November 2022

Characterization of the specific expression and chromatin profiles of genes enables understanding how they contribute to tissue/organ development and the mechanisms leading to diseases. Whilst the number of single-cell sequencing studies is increasing dramatically; however, data mining and reanalysis remains challenging. Herein, we systematically curated the up-to-date and most comprehensive datasets of sequencing data originating from 2760 bulk samples and over 5.1 million single-cells from multiple developmental periods from humans and multiple model organisms. With unified and systematic analysis, we profiled the gene expression and chromatin accessibility among 481 cell-types, 79 tissue-types and 92 timepoints, and pinpointed cells with the co-expression of target genes. We also enabled the detection of gene(s) with a temporal and cell-type specific expression profile that is similar to or distinct from that of a target gene. Additionally, we illustrated the potential upstream and downstream gene−gene regulation interactions, particularly under the same biological process(es) or KEGG pathway(s). Thus, TEDD (Temporal Expression during Development Database), a value-added database with a user-friendly interface, not only enables researchers to identify cell-type/tissue-type specific and temporal gene expression and chromatin profiles but also facilitates the association of genes with undefined biological functions in development and diseases. The database URL is https://TEDD.obg.cuhk.edu.hk/.