bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated Library Construction and Analysis for High-Throughput Nanopore Sequencing of SARS-CoV-2
Authors: Coope Robin J N , Matic Nancy , Pandoh Pawan K , Corbett Richard D , Smailus Duane E , Pleasance Stephen , Lowe Christopher F , Ritchie Gordon , Chorlton Samuel D , Young Matthew , Ally Adrian A , Asano Jennifer K , Carlsen Rebecca E , Chahal Sundeep S , Zhao Yongjun , Holmes Daniel T , Romney Marc G , Jones Steven J M , Marra Marco A
Published: June 2022

Background

To support the implementation of high-throughput pipelines suitable for SARS-CoV-2 sequencing and analysis in a clinical laboratory, we developed an automated sample preparation and analysis workflow.

Methods

We used the established ARTIC protocol with approximately 400 bp amplicons sequenced on Oxford Nanopore’s MinION. Sequences were analyzed using Nextclade, assigning both a clade and quality score to each sample.

Results

A total of 2179 samples on twenty-five 96-well plates were sequenced. Plates of purified RNA were processed within 12 h, sequencing required up to 24 h, and analysis of each pooled plate required 1 h. The use of samples with known threshold cycle (Ct) values enabled normalization, acted as a quality control check, and revealed a strong correlation between sample Ct values and successful analysis, with 85% of samples with Ct < 30 achieving a “good” Nextclade score. Less abundant samples responded to enrichment with the fraction of Ct > 30 samples achieving a “good” classification rising by 60% after addition of a post-ARTIC PCR normalization. Serial dilutions of 3 variant of concern samples, diluted from approximately Ct = 16 to approximately Ct = 50, demonstrated successful sequencing to Ct = 37. The sample set contained a median of 24 mutations per sample and a total of 1281 unique mutations with reduced sequence read coverage noted in some regions of some samples. A total of 10 separate strains were observed in the sample set, including 3 variants of concern prevalent in British Columbia in the spring of 2021.

Conclusions

We demonstrated a robust automated sequencing pipeline that takes advantage of input Ct values to improve reliability.
Extending lactation length: consequences for cow, calf, and farmer
Authors: van Knegsel Ariette T M , Burgers Eline E A , Ma Junnan , Goselink Roselinde M A , Kok Akke
Published: June 2022

Traditionally, a 1-yr calving interval is advised to farmers from an economical point of view, to realize a yearly peak in milk yield. A 1-yr calving interval, however, implies a yearly event of drying-off, calving and start of lactation, which are all associated with an increased risk for diseases and disorders. Deliberately extending the lactation length by extending the voluntary waiting period (VWP) for first insemination reduces the frequency of these challenging events. This reduction in frequency of calvings can be beneficial for cow health and fertility, but also can be of interest to reduce the number of surplus calves and labor associated with drying off, calving, and disease treatments. Current concerns with respect to an extended lactation are that milk yield is too low in late lactation, which might be associated with an increased risk of fattening of cows in late lactation, and compromised economic returns at herd level. In addition, limited knowledge is available with respect to consequences for cow performance in the subsequent lactation and for calves born to cows with an extended lactation. Moreover, response of dairy cows to an extended VWP depends on individual cow characteristics like parity, milk yield level or body condition. A customized strategy based on individual cow characteristics can be a future approach to select high-producing cows with persistent lactation curves for an extended lactation to limit the risk for fattening and milk yield reduction at the end of the lactation while benefitting from a reduction in challenging events around calving.
Revision Surgery Following Severe Frostbite Injury Compared to Similar Hand and Foot Burns
Authors: Coward Alexandra , Endorf Frederick W , Nygaard Rachel M
Published: June 2022

Severe frostbite is associated with loss of digits or limbs and high levels of morbidity. The current practice is to salvage as much of the limb/digit as possible with the use of thrombolytic and adjuvant therapies. Sequelae from amputation can include severe nerve pain and poor wound healing requiring revision surgery. The aim of this study was to examine the rate of revision surgery after primary amputation and compare this to revision surgery in isolated hand/foot burns. Frostbite and burn patients from 2014 to 2019 were identified in the prospectively maintained database at a single urban burn and trauma center. Patients with primary amputations related to isolated hand/foot burns or frostbite were included in the study. Descriptive statistics included Student’s t-test and Fisher’s exact test. A total of 63 patients, 54 frostbite injuries and 9 isolated hand or foot burns, met inclusion criteria for the study. The rate of revision surgery was similar following frostbite and burn injury (24% vs 33%, P = .681). There were no significant differences in age, sex, or length of stay on the primary hospitalization between those that required revision surgery and those that did not. Neither the impacted limb nor the presence of infection or cellulitis on primary amputation was associated with future need for revision surgery. Of the 16 patients requiring revision surgery, 5 (31%) required additional debridement alone, 6 (38%) required reamputation alone, and 5 required both. A total of 6 patients (38%) had cellulitis or infection at the time of revision surgery. Time from primary surgery to revision ranged from 4 days to 3 years. Planned, delayed primary amputation is a mainstay of frostbite management. To our knowledge, this is the first assessment of revision surgery in the setting of severe frostbite injury. Our observed rate of revision surgery following frostbite injury did not differ significantly from revision surgery in the setting of isolated hand or foot burns. This study brings up important questions of timing and surgical planning in these complex patients that will require a multicenter collaborative study.
Chemotherapy Regimens Received by Women With BRCA1/2 Pathogenic Variants for Early Stage Breast Cancer Treatment
Authors: Kurian Allison W , Abrahamse Paul , Hamilton Ann S , Caswell-Jin Jennifer L , Gomez Scarlett L , Hofer Timothy J , Ward Kevin C , Katz Steven J
Published: June 2022

Background

Genetic testing is widespread among breast cancer patients; however, no guideline recommends using germline genetic testing results to select a chemotherapy regimen. It is unknown whether breast cancer patients who carry pathogenic variants (PVs) in BRCA1 and/or 2 (BRCA1/2) or other cancer-associated genes receive different chemotherapy regimens than noncarriers.

Methods

We linked Surveillance, Epidemiology, and End Results registry records from Georgia and California to germline genetic testing results from 4 clinical laboratories. Patients who 1) had stages I-III breast cancer, either hormone receptor (HR) positive and HER2 negative or triple negative (TNBC), diagnosed in 2013-2017; 2) received chemotherapy; and 3) were linked to genetic results were included. Chemotherapy details were extracted from Surveillance, Epidemiology, and End Results text fields completed by registrars. We examined whether PV carriers received more intensive regimens (HR-positive,HER2-negative: ≥3 drugs including an anthracycline; TNBC: ≥4 drugs including an anthracycline and platinum) and/or less standard breast cancer agents (a platinum). All statistical tests were 2-sided.

Results

Among 2293 patients, 1451 had HR-positive, HER2-negative disease, and 842 had TNBC. On multivariable analysis of women with HR-positive, HER2-negative disease, receipt of a more intensive chemotherapy regimen varied statistically significantly by genetic results (P = .02), with platinum receipt more common among BRCA1/2 PV carriers (odds ratio = 2.44, 95% confidence interval = 1.36 to 4.38; P < .001). Among women with TNBC, chemotherapy agents did not vary significantly by genetic results.

Conclusion

BRCA1/2 PV carriers with HR-positive, HER2-negative breast cancer had twofold higher odds than noncarriers of receiving a platinum, as part of a more intensive chemotherapy regimen. This likely represents overtreatment and emphasizes the need to monitor how genetic testing results are managed in oncology practice.
Botany, traditional uses, phytochemistry, pharmacological and toxicological effects of Croton tiglium Linn.: a comprehensive review
Authors: Zhang Ting , Liu Zibo , Sun Xue , Liu Ziqi , Zhang Lilin , Zhang Qing , Peng Wei , Wu Chunjie
Published: June 2022

Objectives

Croton tiglium Linn. (Euphorbiaceae) is an ancient medicinal plant that has been used for a long time, which is widely distributed in tropical and subtropical regions. And it is widely used for defecation, induced labour, treatment of gastrointestinal diseases, headache, as well as rheumatoid arthritis.

Key findings

Approximately 150 compounds have been isolated and identified from the seeds, stems, leaves and branches of C. tiglium, including fatty acids, terpenoids, alkaloids, the plants proteins and other types of components. Based on a wide range of biological properties, C. tiglium has a wide range of pharmacological effects, such as antitumor, anti-HIV, analgesic, anti-inflammatory and antibacterial effects.

The review aims to provide a critical and comprehensive evaluation of the botany, phytochemistry, pharmacology and toxicity of C. tiglium, with a vision for promoting further pharmaceutical research to explore its complete potential for better clinical application. The tigliane diterpenoids have been the most studied compounds isolated from C. tiglium, which showing a variety of biological activities, but there is insufficient evidence to explain the mechanism of action. In addition, C. tiglium may have potential toxic effects, and it is necessary to reduce the toxic effects to ensure the safety of clinical medication, which may promote the discovery and development of new drugs.
Empirically motivated early feedback: momentum input by stellar feedback in galaxy simulations inferred through observations
Authors: Keller Benjamin W , Kruijssen J M Diederik , Chevance Mélanie
Published: June 2022

We present a novel method for including the effects of early (pre-supernova) feedback in simulations of galaxy evolution. Rather than building a model which attempts to match idealized, small-scale simulations or analytic approximations, we rely on direct observational measurements of the time-scales over which star-forming molecular clouds are disrupted by early feedback. We combine observations of the spatial de-correlation between molecular gas and star formation tracers on ∼100 pc scales with an analytic framework for the expansion of feedback fronts driven by arbitrary sources or mechanisms, and use these to constrain the time-scale and momentum injection rate by early feedback. This allows us to directly inform our model for feedback from these observations, sidestepping the complexity of multiple feedback mechanisms and their interaction below the resolution scale. We demonstrate that this new model has significant effects on the spatial clustering of star formation, the structure of the ISM, and the driving of outflows from the galactic plane, while preserving the overall regulation of the galaxy-integrated star formation rate. We find that this new feedback model results in galaxies that regulate star formation through the rapid disruption of star-forming clouds, rather than by highly efficient, global galactic outflows. We also demonstrate that these results are robust to stochasticity, degraded numerical resolution, changes in the star formation model parameters, and variations in the single free model parameter that is unconstrained by observations.
The Sloan Digital Sky Survey peculiar velocity catalogue
Authors: Howlett Cullan , Said Khaled , Lucey John R , Colless Matthew , Qin Fei , Lai Yan , Tully R Brent , Davis Tamara M
Published: June 2022

We present a new catalogue of distances and peculiar velocities (PVs) of 34 059 early-type galaxies derived from fundamental plane (FP) measurements using data from the Sloan Digital Sky Survey (SDSS). This $7016\, \mathrm{deg}^{2}$ homogeneous sample comprises the largest set of PVs produced to date and extends the reach of PV surveys up to a redshift limit of z = 0.1. Our SDSS-based FP distance measurements have a mean uncertainty of 23 per cent. Alongside the data, we produce an ensemble of 2048 mock galaxy catalogues that reproduce the data selection function, and are used to validate our fitting pipelines and check for systematic errors. We uncover a significant trend between group richness and mean surface brightness within the sample, which may hint at an environmental dependence within the FP or the presence of unresolved systematics, and can result in biased PVs. This is removed by using multiple FP fits as function of group richness, a procedure made tractable through a new analytic derivation for the integral of a three-dimensional (3D) Gaussian over non-trivial limits. Our catalogue is calibrated to the zero-point of the CosmicFlows-III sample with an uncertainty of 0.004 dex (not including cosmic variance or the error within CosmicFlows-III itself), which is validated using independent cross-checks with the predicted zero-point from the 2M++ reconstruction of our local velocity field. Finally, as an example of what is possible with our new catalogue, we obtain preliminary bulk flow measurements up to a depth of $135\,{\rm h}^{-1}\mathrm{Mpc}$. We find a slightly larger-than-expected bulk flow at high redshift, although this could be caused by the presence of the Shapley supercluster, which lies outside the SDSS PV footprint.
The dark energy survey 5-yr photometrically identified type Ia supernovae
Authors: Möller A , Smith M , Sako M , Sullivan M , Vincenzi M , Wiseman P , Armstrong P , Asorey J , Brout D , Carollo D , Davis T M , Frohmaier C , Galbany L , Glazebrook K , Kelsey L , Kessler R , Lewis G F , Lidman C , Malik U , Nichol R C , Scolnic D , Tucker B E , Abbott T M C , Aguena M , Allam S , Annis J , Bertin E , Bocquet S , Brooks D , Burke D L , Carnero Rosell A , Carrasco Kind M , Carretero J , Castander F J , Conselice C , Costanzi M , Crocce M , da Costa L N , De Vicente J , Desai S , Diehl H T , Doel P , Everett S , Ferrero I , Finley D A , Flaugher B , Friedel D , Frieman J , García-Bellido J , Gerdes D W , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Herner K , Hinton S R , Hollowood D L , Honscheid K , James D J , Kuehn K , Kuropatkin N , Lahav O , March M , Marshall J L , Menanteau F , Miquel R , Morgan R , Palmese A , Paz-Chinchón F , Pieres A , Plazas Malagón A A , Romer A K , Roodman A , Sanchez E , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Suchyta E , Tarle G , Thomas D , To C , Varga T N
Published: June 2022

As part of the cosmology analysis using Type Ia Supernovae (SN Ia) in the Dark Energy Survey (DES), we present photometrically identified SN Ia samples using multiband light curves and host galaxy redshifts. For this analysis, we use the photometric classification framework SuperNNovatrained on realistic DES-like simulations. For reliable classification, we process the DES SN programme (DES-SN) data and introduce improvements to the classifier architecture, obtaining classification accuracies of more than 98 per cent on simulations. This is the first SN classification to make use of ensemble methods, resulting in more robust samples. Using photometry, host galaxy redshifts, and a classification probability requirement, we identify 1863 SNe Ia from which we select 1484 cosmology-grade SNe Ia spanning the redshift range of 0.07 < z < 1.14. We find good agreement between the light-curve properties of the photometrically selected sample and simulations. Additionally, we create similar SN Ia samples using two types of Bayesian Neural Network classifiers that provide uncertainties on the classification probabilities. We test the feasibility of using these uncertainties as indicators for out-of-distribution candidates and model confidence. Finally, we discuss the implications of photometric samples and classification methods for future surveys such as Vera C. Rubin Observatory Legacy Survey of Space and Time.
Identifying the population of stable ν6 resonant asteroids using large data bases
Authors: Carruba V , Aljbaae S , Domingos R C , Huaman M , Martins B
Published: June 2022

Large observational surveys, like those that will be conducted at the Vera C. Rubin Observatory, are expected to discover up to one million new asteroids in the first year of operation. This will more than double the data base of known asteroids. New methods will be needed to handle the large influx of data. Here, we tested some of these new approaches by studying the population of asteroids on stable orbits inside the ν6 secular resonance. This resonance is one of the strongest mechanisms for destabilizing the orbits of main-belt bodies and producing Near-Earth Asteroids. Yet, stable orbital configurations where the asteroid pericenter is either aligned or anti-aligned with that of Saturn exist inside the resonance. The population of stable ν6 resonators is now the largest population of asteroids in stable orbits inside a secular resonance. Here, we obtained the largest sample of asteroids’ proper elements ever used. Clustering methods and the use of machine learning algorithms permitted the identification of the known asteroid families crossed by the ν6 resonance and of two entirely new groups: the Tiffanykapler and the 138605 QW177 families. The Tiffanykapler family is the first young asteroid family ever found in a linear secular resonance, with an age of 3.0 ± 1.2 My and an ejection velocity field parameter of $V_{\mathrm{ EJ}} = 15^{+6}_{-3}$ m s−1. We identify a population of high-eccentricity objects around the Tina family that may be the first example of an asteroid family ‘resonant halo’.
Improved statistic to identify strongly lensed gravitational wave events
Authors: More Anupreeta , More Surhud
Published: June 2022

As the number of detected gravitational wave sources increases with increased sensitivity of the gravitational wave observatories, observing strongly lensed pairs of events will become a real possibility. Lensed gravitational wave (GW) events will have very accurately measured time delays and magnification ratios. Suppose we identify the lens system corresponding to a GW event in the electromagnetic domain and also measure the redshifts of the lens and the host galaxy; in that case, we can use the GW event to constrain important astrophysical parameters of the lens system. As most lensing events have image separations that are significantly smaller than the GW event localization uncertainties, we must develop diagnostics that will aid in the robust identification of such lensed events. We define a new statistic based on the joint probability of lensing observables that can be used to discriminate lensed pairs of events from the unlensed ones. To this end, we carry out simulations of lensed GW events to infer the distribution of the relative time delays and relative magnifications subdivided by the type of lensed images. We compare this distribution to a similar one obtained for random unlensed event pairs. Our statistic can improve the search pipelines’ existing ranking approach to down-select event pairs for joint parameter estimates. The distributions we obtain can further be used to define more informative priors in joint parameter estimation analyses for candidate lensed events.
Large trees and forest heterogeneity facilitate prey capture by California Spotted Owls
Authors: Zulla Ceeanna J , Kramer H Anu , Jones Gavin M , Keane John J , Roberts Kevin N , Dotters Brian P , Sawyer Sarah C , Whitmore Sheila A , Berigan William J , Kelly Kevin G , Wray Amy K , Peery M Zachariah
Published: June 2022

Predators are among the most threatened animal groups globally, with prey declines contributing to their endangerment. However, assessments of the habitat conditions that influence the successful capture of different prey species are rare, especially for small, cryptic predators. Accordingly, most predator conservation plans are based on the relative importance of habitats inferred from coarse-scale studies that do not consider habitat features contributing to hunting success, which can vary among prey species. To address this limitation, we integrated high-resolution global positioning system tracking and nest video monitoring to characterize habitat features at prey capture locations during the nestling provisioning stage for the Spotted Owl (Strix occidentalis) a small, cryptic predator that has been at the center of a decades-long forest management conflict in western North America. When all prey species were considered collectively, males provisioning nests tended to capture prey: (1) in areas with more large-tree forest, (2) in areas with more medium trees/medium canopy forest, and (3) at edges between conifer and hardwood forests. However, when we considered the owl’s two key prey species separately, males captured woodrats (Neotoma fuscipes) and Humboldt flying squirrels (Glaucomys oregonensis) in areas with markedly different habitat features. Our study provides clarity for forest management in mixed-ownership landscapes because different prey species achieve high densities in different habitat types. Specifically, our results suggest that promoting large trees, increasing forest heterogeneity, and creating canopy gaps in forests with medium trees/high canopy cover could benefit Spotted Owls and their prey, which has the ancillary benefit of enhancing forest resilience. Combining high-resolution global positioning system tagging with video-based information on prey deliveries to breeding sites can strengthen conservation planning for small predators by more rigorously defining those habitat features that are associated with successful prey acquisition.
Perceptions of risk in people with inflammatory arthritis during the COVID-19 pandemic
Authors: Ryan Sarah , Campbell Paul , Paskins Zoe , Manning Fay , Rule Katrina , Brooks Michael , Hider Samantha , Hassell Andrew
Published: June 2022

Objective

People with inflammatory arthritis have an increased incidence of serious illness and mortality, placing them at risk of poor outcomes from coronavirus disease 2019 (COVID-19). This study explored patients’ perceptions of risk from COVID-19 over a longitudinal period of the pandemic.

Methods

Fifteen adults with inflammatory arthritis attending a National Health Service rheumatology service each took part in three semi-structured telephone interviews conducted between 16 September 2020 and 29 July 2021. Interpretive phenomenological analysis was undertaken by two researchers and two public contributors.

Results

Four main themes relating to perceptions of risk from COVID-19 were identified: inflammatory arthritis; medications and co-morbidities; immediate social environment; health policy communication; and media influence. Participants recognized that having inflammatory arthritis increased their individual risk. Perceptions of risk and associated fear increased during the pandemic, influenced by family/friends who had had COVID-19 and health policy communications. The perceived constant use of negative messages led to many participants disengaging with the media. At the final interviews, when the vaccination programme was well established, participants continued to assess the risk and benefits of engaging in activities.

Conclusion

This study demonstrates the breadth of factors that influenced perceptions of risk in people with an inflammatory arthritis. As health professionals, we have only a small sphere of influence over some of these factors, namely health-care communications. People with inflammatory arthritis appropriately knew that their condition increased their infection risk, but more could be done to consider how and to what extent we involve patients in explaining risk at times of crisis.
Technology, Skills, and Globalization: Explaining International Differences in Routine and Nonroutine Work Using Survey Data
Authors: Lewandowski Piotr , Park Albert , Hardy Wojciech , Du Yang , Wu Saier
Published: June 2022

The shift from routine work to nonroutine cognitive work is a key feature of labor markets globally, but there is little evidence on the extent to which tasks differ among workers performing the same jobs in different countries. This paper constructs survey-based measures of routine task intensity (RTI) of jobs consistent with those based on the U.S. O*NET database for workers in 47 countries. It confirms substantial cross-country differences in the content of work within occupations. The extent to which workers’ RTI is predicted by technology, supply of skills, globalization, and economic structure is assessed; and their contribution to the variation in RTI across countries is quantified. Technology is by far the most important factor. Supply of skills is next in importance, especially for workers in high-skilled occupations, while globalization is more important than skills for workers in low-skilled occupations. Occupational structure explains only about one-fifth of cross-country variation in RTI.
Passaging Phyllosphere Microbial Communities Develop Suppression Towards Bacterial Speck Disease in Tomato
Authors: Ehau-Taumaunu Hanareia , Hockett Kevin L.
Published: June 2022

Microbial community-based disease management approaches have the potential to substitute or combine with currently employed strategies. Suppressive soils are great examples of microbial communities that suppress soilborne plant disease after severe outbreaks and are maintained over multiple years or crop cycles. Although there are many suppressive soil examples, to our knowledge, there are no descriptions of disease-suppressive phyllosphere communities. Therefore, we investigated whether a phyllosphere microbial community could be developed through a selective passaging method to suppress disease using the model pathosystem of Pseudomonas syringae pv. tomato ( Pto) and tomato. Field tomato phyllosphere microbial communities were recovered and spray transferred to greenhouse tomato plants, after which they were inoculated with Pto. Disease severity was visually estimated and the microbial communities were recovered to be independently applied to the next passage. Overall, greenhouse passaging resulted in an increase in disease severity for all passage lines from the initial passage, which peaked at passage 4 to 5, followed by a sharp decline until passage 9. The disease severity at passage 9 was also significantly lower than a non-passaged Pto-only comparison. Heat treatment of passage 9 communities resulted in elevated disease severity over several subsequent passages in the growth chamber, whereas the untreated community maintained low disease. Community-only passage lines (without Pto inclusion during passaging) did not show disease suppression after subsequent pathogen introduction. This work presents an experimental approach to develop phyllosphere microbial communities in the presence of a phytopathogen to enrich for a low disease phenotype and results in maintained disease suppression.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Optimizing Molecular Detection for the Hop Downy Mildew Pathogen Pseudoperonospora humuli in Plant Tissue
Authors: Higgins Douglas S. , Miles Timothy D. , Byrne Jan M. , Hausbeck Mary K.
Published: June 2022

Downy mildew-free hop plantlets and rhizomes are essential to limit the introduction of this destructive pathogen, Pseudoperonospora humuli, into hopyards. The objective of this research was to determine which DNA-based diagnostic tools are optimal for P. humuli detection in plant tissue. Quantitative real-time PCR (qPCR) assays with TaqMan probes for nuclear ( c125015.3e1) and mitochondrial ( orf359) DNA loci were developed and tested side by side. A recombinase polymerase amplification (RPA) assay was designed based on the orf359 DNA locus. The mitochondrial qPCR assay had a 10-fold lower limit of detection (100 fg of genomic DNA) and was 60% more effective in detecting P. humuli in asymptomatic stems than the nuclear-based assay. Both qPCR assays had linear standard curves ( R2 > 0.99) but lacked the quantitative precision to differentiate leaf infections beyond 1 day postinoculation. A wide range of Cq values (≥4.9) in standardized tests was observed among isolates, suggesting that the number of mitochondria and nuclear DNA targets can vary. The absence of P. humuli DNA in symptomatic rhizomes was explained, in part, by the detection of Phytophthora DNA. However, the Phytophthora-specific atp9-nad9 assay cross-reacted with P. humuli, leading to false positive amplification. Sensitivity in the RPA assay was reduced by crude plant DNA extract. Improvements to the objectivity of calling positive amplifications and determining the onset of amplification from RPA fluorescence data were realized by applying the first and second derivatives, respectively. The orf359 qPCR assay is specific and sensitive, making it well suited for P. humuli diagnostics in plant tissue.
Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses
Authors: Moubset Oumaima , François Sarah , Maclot François , Palanga Essowè , Julian Charlotte , Claude Lisa , Fernandez Emmanuel , Rott Philippe , Daugrois Jean-Heinrich , Antoine-Lorquin Aymeric , Bernardo Pauline , Blouin Arnaud G. , Temple Coline , Kraberger Simona , Fontenele Rafaela S. , Harkins Gordon W. , Ma Yuxin , Marais Armelle , Candresse Thierry , Chéhida Sélim Ben , Lefeuvre Pierre , Lett Jean-Michel , Varsani Arvind , Massart Sébastien , Ogliastro Mylène , Martin Darren P. , Filloux Denis , Roumagnac Philippe
Published: June 2022

Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Are Digital Arthroplasty and Arthrodesis Useful and Safe Surgical Techniques for the Management of Patients with Diabetic Foot?
Authors: Tardáguila-García Aroa , Sanz-Corbalán Irene , López-Moral Mateo , García-Madrid Marta , García-Morales Esther , Lázaro-Martínez José Luis
Published: June 2022

OBJECTIVE

To analyze and compare the development of short- and long-term complications in patients with diabetic foot after digital arthroplasty or arthrodesis.

METHODS

The authors reviewed patient records from January 2017 to March 2020. Patients were treated by digital arthroplasty or arthrodesis to correct toe deformity (elective or prophylactic surgery), achieve ulcer healing in toes (curative surgery), or manage toe infection (emergent surgery). During 1-year follow-up, researchers registered short- and long-term complications. Researchers analyzed the association between the type of surgery and the development of short- and long-term complications.

RESULTS

Forty-four patients (83.0%) received arthroplasty, and nine (17.0%) received arthrodesis. The mean time to heal from ulcers was 5.2 ± 5.2 weeks. A significant association was observed between arthrodesis and the development of long-term complications (P = .044; odds ratio, 5.1; 95% confidence interval, 0.9–27.2). No differences were observed between type of surgery and short- or long-term complications. Moreover, both short- and long-term complications were related to longer time to heal (respectively, 7.6 ± 6.0 vs 2.1 ± 0.5 weeks, P < .001; and 6.3 ± 6.2 vs 4.2 ± 4.0 weeks, P = .039).

CONCLUSIONS

Digital arthroplasty or arthrodesis are good options for managing patients with diabetic foot who require digital deformity correction to achieve digital ulcer healing or management of diabetic foot infection in phalanges.
Second-Intention Healing in Mohs Micrographic Surgery: A Single-Center Academic Experience
Authors: Barrera-Llaurador Julián , Carrasquillo Osward Y. , Santiago-Vázquez Marely , González-Molina Valeria J. , Valentín-Nogueras Sheila M.
Published: June 2022

OBJECTIVE

To describe the trends in second-intention healing (SIH) use at a single Mohs micrographic surgery (MMS) dermatology clinic and assess outcomes and patient satisfaction.

METHODS

The authors conducted a single-center, retrospective study of patients who underwent MMS from November 2012 through November 2018. Data obtained for each patient included sex, age, tumor characteristics, number of MMS stages, final defect size, and postoperative complications. Patient satisfaction of SIH was retrospectively assessed by telephone survey.

RESULTS

Providers used SIH in 22% of all MMS cases (n = 159/718). It was most commonly used for defects located on the nose, ear, temple, and periocular region. The average defect size and number of MMS stages for tumor clearance were 1.3 cm and 1.5 stages, respectively. Overall, low rates of postoperative complications were observed, and 95% of patients reported optimal or acceptable levels of satisfaction.

CONCLUSIONS

This study supports the idea that SIH is a safe, effective alternative for wound management and may have broader practice indications than those traditionally proposed.
Evaluating Equity Through the Social Determinants of Hearing Health
Authors: Schuh Marissa R. , Bush Matthew L.
Published: June 2022

Hearing loss in adults is a significant public health problem throughout the world. Undiagnosed and untreated hearing loss causes a measurable impact on health and social, occupational, and emotional well-being of those affected. In spite of a wide array of health care resources to identify and manage hearing loss, there exist vast disparities in outcomes, as well as access to and utilization of hearing healthcare. Hearing rehabilitation outcomes may vary widely among different populations and there is a pressing need to understand, in a broader sense, the factors that influence equitable outcomes, access, and utilization. These factors can be categorized according to the widely accepted framework of social determinants of health, which is defined by the World Health Organization as “the conditions in which people are born, grow, work, live, and age.” According to Healthy People 2030, these determinants can be broken into the following domains: healthcare access and quality, education access and quality, social and community context, economic stability, and neighborhood and built environment. This article defines these domains and examines the published research and the gaps in research of each of these domains, as it pertains to hearing health and healthcare. Herein, we review foundational sources on the social determinants of health and hearing-related research focused on the topic. Further consideration is given to how these factors can be evaluated in a systematic fashion and be incorporated into translational research and hearing health care.
Anterograde Injection of Alteplase Salvages Deep Inferior Epigastric Perforator Flap in Reconstructive Breast Surgery
Authors: Wimbauer Julia M. , Heinrich Klemens M. , Schwaiger Karl , Pumberger Peter , Koeninger Fabian , Wechselberger Gottfried , Russe Elisabeth
Published: June 2022

The DIEP flap is currently considered the gold standard for autologous reconstructive breast surgery. Postoperative flap failure due to microvascular postanastomotic thrombotic occlusion is a rare but severe complication. Alteplase, a thrombolytic agent typically used in the setting of an ischemic stroke, myocardial infarction, or pulmonary embolism, has also been injected into the microcirculation of flaps as a rescue procedure due to imminent flap loss. The purpose of this article is to provide an overview and detailed guidance for such a thrombolytic procedure due to suspected thrombotic microsurgical failure in free flap surgery. We report the case of a 43-year-old woman who underwent unilateral breast reconstruction with a DIEP flap at our department. Approximately 12 hours postoperatively, an arterial inflow problem was suspected and revision surgery was performed. Peripheral flap perfusion remained absent without an obvious cause and distal thrombosis was assumed to be present. Therefore, alteplase was gradually injected into the arterial pedicle in the anterograde direction just distal to the anastomosis while clamping the artery proximally. About 3 hours after selective flap thrombolysis, microcirculation of the flap was successfully restored without complications. Anterograde injection of alteplase can successfully salvage a free flap. To our knowledge, evidence for optimal dosing and delivery of alteplase for the treatment of thrombosed DIEP flaps has not been published to date. Our approach presents a therapeutic option that both maximizes alteplase concentration in the flap and minimizes the dosage required for flap salvage to significantly reduce systemic adverse effects.
COVID-19-induced Scalp Alopecia Treated Effectively with Stem Cell Serum
Authors: Ong Samuel Wei Qiang , Ong Kathleen Hui Xin , Lee Shu Jin
Published: June 2022

Up to 36.7% of symptomatic COVID-19 patients will have telogen effluvium (TE), which refers to diffuse scalp alopecia. With the continuing global pandemic, a review of literature reports unpredictable and incomplete recovery with conventional treatment like minoxidil. The pathogenesis of COVID-19-induced TE may be more severe than that of conventional TE as the hair follicles are proposed to be directly damaged by cytokines and thromboembolism. There is no current standardized treatment for COVID-19-induced TE. We present a patient with severe chronic TE, with no spontaneous recovery after 6 months of hair loss and minimal response to minoxidil. We commenced monthly applications of stem cell serum (Calecim). We present the results of five treatments spaced monthly, after which he experienced effective regrowth of scalp hair. We propose stem cell serum for patients who have failed conventional treatment or as an adjunct to conventional therapy in COVID-19-induced TE.
Return to Full Participation Following Concussion in the National Football League, 2015 Through 2020
Authors: Mack Christina D. , Herzog Mackenzie M. , Solomon Gary , Putukian Margot , Lee Rebecca Y. , Matava Matthew J. , Cárdenas Javier , Theodore Nicholas , Sills Allen
Published: June 2022

Objective:

Quantify days missed, games missed, injury burden, and time to return to full participation (RTFP) among National Football League (NFL) players who sustained a concussion.

Design:

Retrospective cohort study.

Setting:

2015 through 2020 NFL seasons.

Participants:

National Football League players diagnosed with a concussion from 2015 to 2020.

Interventions:

National Football League-mandated graduated RTFP protocol.

Main Outcome Measures:

Days missed, games missed, burden, and time to RTFP, overall and by position.

Results:

An annual average of 3639 player-days of participation and 255 games were missed across NFL because of concussion. Concussed players missed a median of 9 days (mean = 15.0), a relatively stable metric over 6 years, with slight variation by position. Offensive linemen, tight ends, running backs, and linebackers missed the most days per concussion; defensive secondary, offensive linemen, and wide receivers sustained the highest injury burden. Postconcussion, 59% of players missed one or more scheduled games. Among players concussed in a Sunday game, 38% played in a Sunday game one week later.

Conclusions:

The 9-day median time missed post-concussion may be related to emphasis on graduated phase-based concussion management. No concussed player returned to competition on the day of injury, and less than 40% participated in games the following week. Further work is needed to better understand characteristics of concussions that take longer to return and movement through stages of return.
Recent insights into the management of treatment-resistant pediatric atopic dermatitis
Authors: Naik Piyu Parth
Published: June 2022

Atopic dermatitis (AD) is a prevalent protracted inflammatory skin condition that affects approximately 12% of children globally. Topical remedies, such as pharmacologic and nonpharmacologic management, and off-label systemic medicines, have traditionally been used to treat pediatric AD patients. To minimize comorbidities, sleep disturbances, pruritus, and signs of inflammation and improve the patient’s quality of life, it is vital to optimize severe AD management in pediatric patients. Treatment resistance can be caused by a variety of circumstances, including deficient obedience or inappropriate medicine usage, a shortage of adequate pharmaceuticals, hypersensitivity reciprocation to local application of therapeutics, cutaneous infections, and other infuriating ecological provoking factors. If these elements are eliminated, a skin biopsy is required to exclude other AD-like cutaneous disorders. New regimens that target peculiar avenues with improved proficiency and promise minimal adverse events have resulted from recent developments and understanding of the etiology of AD. Although the condition of most patients improves quickly with this treatment, some do not respond well. In this review, the author discusses the management of treatment-resistant atopic dermatitis, with an emphasis on the pediatric population.
Imaging of the Left Atrial Appendage Before Occluder Device Placement: Evaluation of Virtual Monoenergetic Images in a Single-Bolus Dual-Phase Protocol
Authors: Laukamp Kai Roman , Dastmalchian Sara , Tandon Yasmeen K. , Ciancibello Leslie , Pennig Lenhard , Lennartz Simon , Al-Kindi Sadeer , Rajagopalan Sanjay , Bera Kaustav , Hokamp Nils Große , Gilkeson Robert , Gupta Amit
Published: June 2022

Purpose

Preimplantation cardiac computed tomography (CT) for assessment of the left atrial appendage (LAA) enables correct sizing of the device and the detection of contraindications, such as thrombi. In the arterial phase, distinction between false filling defects and true thrombi can be hampered by insufficient contrast medium distribution. A delayed scan can be used to further differentiate both conditions, but contrast in these acquisitions is relatively lower. In this study, we investigated whether virtual monoenergetic images (VMI) from dual-energy spectral detector CT (SDCT) can be used to enhance contrast and visualization in the delayed phase.

Materials and Methods

Forty-nine patients receiving SDCT imaging of the LAA were retrospectively enrolled. The imaging protocol comprised dual-phase acquisitions with single-bolus contrast injection. Conventional images (CI) from both phases and 40-keV VMI from the delayed phase were reconstructed. Attenuation, signal-, and contrast-to-noise ratios (SNR/CNR) were calculated by placing regions-of-interest in the LAA, left atrium, and muscular portion of interventricular septum. Two radiologists subjectively evaluated conspicuity and homogeneity of contrast distribution within the LAA.

Results

Contrast of the LAA decreased significantly in the delayed phase but was significantly improved by VMI, showing comparable attenuation, SNR, and CNR to CI from the arterial phase (attenuation/SNR/CNR, CI arterial phase: 266.0 ± 117.0 HU/14.2 ± 7.2/6.6 ± 3.9; CI-delayed phase: 107.6 ± 35.0 HU/5.9 ± 3.0/1.0 ± 1.0; VMI delayed phase: 260.3 ± 108.6 HU/18.2 ± 10.6/4.8 ± 3.4). The subjective reading confirmed the objective findings showing improved conspicuity and homogeneity in the delayed phase.

Conclusions

The investigated single-bolus dual-phase acquisition protocol provided improved visualization of the LAA. Homogeneity of contrast media was higher in the delayed phase, while VMI maintained high contrast.
Spectral invariants of ergodic symbolic systems for pattern recognition and anomaly detection
Authors: Ghalyan Najah F. , Bhattacharya Chandrachur , Ghalyan Ibrahim F. , Ray Asok
Published: June 2022

Despite tangible advances in machine learning (ML) over the last few decades, many of the ML techniques still suffer from fundamental issues like overfitting and lack of explainability. These issues mandate requirements for mathematical rigor to ensure robust learning from observed data. In this context, topological invariants in data manifolds provide a rich representation of the underlying dynamical system, which can be utilized for developing a mathematically rigorous ML tool to characterize the dynamical behaviour and operational phases of the underlying process. This paper aims to investigate spectral invariants of symbolic systems for detecting changes in topological characteristics of data manifolds. A novel ML approach is proposed, where commutator norms are used on sequences of endomorphisms to symbolically describe dynamical systems on probability spaces with ergodic measures. The objective here is to detect topological invariants of data manifolds that can be used for signal processing, pattern recognition, and anomaly detection. The proposed ML approach is validated on models of selected chaotic dynamical systems for prompt detection of phase transitions.

This article is part of the theme issue ‘Data-driven prediction in dynamical systems’.
Machine learning-based statistical closure models for turbulent dynamical systems
Authors: Qi Di , Harlim John
Published: June 2022

We propose a machine learning (ML) non-Markovian closure modelling framework for accurate predictions of statistical responses of turbulent dynamical systems subjected to external forcings. One of the difficulties in this statistical closure problem is the lack of training data, which is a configuration that is not desirable in supervised learning with neural network models. In this study with the 40-dimensional Lorenz-96 model, the shortage of data is due to the stationarity of the statistics beyond the decorrelation time. Thus, the only informative content in the training data is from the short-time transient statistics. We adopt a unified closure framework on various truncation regimes, including and excluding the detailed dynamical equations for the variances. The closure framework employs a Long-Short-Term-Memory architecture to represent the higher-order unresolved statistical feedbacks with a choice of ansatz that accounts for the intrinsic instability yet produces stable long-time predictions. We found that this unified agnostic ML approach performs well under various truncation scenarios. Numerically, it is shown that the ML closure model can accurately predict the long-time statistical responses subjected to various time-dependent external forces that have larger maximum forcing amplitudes and are not in the training dataset.

This article is part of the theme issue ‘Data-driven prediction in dynamical systems’.