bluuebunny/crossref_metadata_2025 huggingface dataset:
Velocity structure functions in multiphase turbulence: interpreting kinematics of Hα filaments in cool-core clusters
Authors: Mohapatra Rajsekhar , Jetti Mrinal , Sharma Prateek , Federrath Christoph
Published: November 2021

The central regions of cool-core galaxy clusters harbour multiphase gas, with gas temperatures ranging from $10$ to $10^7\, \mathrm{K}$. Feedback from active galactic nuclei jets prevents the gas from undergoing a catastrophic cooling flow. However, the exact mechanism of this feedback energy input is unknown, mainly due to the lack of velocity measurements of the hot-phase gas. However, recent observations have measured the velocity structure functions (VSFs) of the cooler molecular (${\sim} 10\, \mathrm{K}$) and Hα filaments (${\sim} 10^4\, \mathrm{K}$) and used them to indirectly estimate the motions of the hot phase. In the first part of this study, we conduct high-resolution (3843–15363 resolution elements) simulations of homogeneous isotropic subsonic turbulence, without radiative cooling. We analyse the second-order velocity structure functions (VSF2) in these simulations and study the effects of varying spatial resolution, the introduction of magnetic fields, and the effect of projection along the line of sight (LOS) on it. In the second part of the study, we analyse high-resolution (7683 resolution elements) idealized simulations of multiphase turbulence in the intracluster medium from the companion study Mohapatra et al. We compare the VSF2 for both the hot ($T\sim 10^7\, \mathrm{K}$) and cold ($T\sim 10^4\, \mathrm{K}$) phases and find that their amplitude depends on the density contrast between the phases. They have similar scaling with separation, but introducing magnetic fields steepens the VSF2 of only the cold phase. We also find that projection along the LOS steepens the VSF2 for the hot phase and mostly flattens it for the cold phase.
Secular evolution of MHD wind-driven discs: analytical solutions in the expanded α-framework
Authors: Tabone Benoît , Rosotti Giovanni P , Cridland Alexander J , Armitage Philip J , Lodato Giuseppe
Published: November 2021

The evolution of protoplanetary discs and the related process of planet formation is regulated by angular momentum transport and mass-loss processes. Over the past decade, the paradigm of viscosity has been challenged and MHD disc winds appear as a compelling scenario to account for disc accretion. In this work, we aim to construct the equivalent of the widely used analytical description of viscous evolution for the MHD wind case. The transport of angular momentum and mass induced by the wind is parametrized by an α-like parameter and by the magnetic lever arm parameter λ. Extensions of the paradigmatic Lynden-Bell and Pringle similarity solutions to the wind case are presented. We show that wind-driven accretion leads to a steeper decrease in the disc mass and accretion rate than in viscous models due to the absence of disc spreading. If the decline of the magnetic field strength is slower than that of the gas surface density, the disc is dispersed after a finite time. The evolution of the disc in the $\dot{M}_*-M_{D}$ plane is sensitive to the wind and turbulence parameters. A disc population evolving under the action of winds can exhibit a correlation between $\dot{M}_*$ and MD depending on the initial conditions. The simplified framework proposed in this work opens to a new avenue to test the effectiveness of wind-driven accretion from the observed disc demographics and constitutes an important step to include wind-driven accretion in planet population synthesis models.
The PG-RQS survey. Building the radio spectral distribution of radio-quiet quasars. I. The 45-GHz data
Authors: Baldi R D , Laor A , Behar E , Horesh A , Panessa F , McHardy I , Kimball A
Published: November 2021

The origin of the radio emission in radio-quiet quasars (RQQs) remains unclear. Radio emission may be produced by a scaled-down version of the relativistic jets observed in radio-loud (RL) AGN, an AGN-driven wind, the accretion disc corona, AGN photon-ionization of ambient gas (free–free emission), or star formation (SF). Here, we report a pilot study, part of a radio survey (‘PG-RQS’) aiming at exploring the spectral distributions of the 71 Palomar–Green (PG) RQQs: high angular resolution observations (∼50 mas) at 45 GHz (7 mm) with the Karl G. Jansky Very Large Array of 15 sources. Sub-mJy radio cores are detected in 13 sources on a typical scale of ∼100 pc, which excludes significant contribution from galaxy-scale SF. For 9 sources the 45-GHz luminosity is above the lower frequency (∼1–10 GHz) spectral extrapolation, indicating the emergence of an additional flatter-spectrum compact component at high frequencies. The X-ray luminosity and black hole (BH) mass, correlate more tightly with the 45-GHz luminosity than the 5-GHz. The 45 GHz-based radio-loudness increases with decreasing Eddington ratio and increasing BH mass MBH. These results suggest that the 45-GHz emission from PG RQQs nuclei originates from the innermost region of the core, probably from the accretion disc corona. Increasing contributions to 45-GHz emission from a jet at higher MBH and lower Eddington ratios and from a disc wind at large Eddington ratios are still consistent with our results. Future full radio spectral coverage of the sample will help us investigating the different physical mechanisms in place in RQQ cores.
No evidence for a strong decrease of planetesimal accretion in old white dwarfs
Authors: Blouin Simon , Xu (许偲艺) Siyi
Published: November 2021

A large fraction of white dwarfs are accreting or have recently accreted rocky material from their planetary systems, thereby ‘polluting’ their atmospheres with elements heavier than helium. In recent years, the quest for mechanisms that can deliver planetesimals to the immediate vicinity of their central white dwarfs has stimulated a flurry of modelling efforts. The observed time evolution of the accretion rates of white dwarfs through their multi-Gyr lifetime is a crucial test for dynamical models of evolved planetary systems. Recent studies of cool white dwarf samples have identified a significant decrease of the mass accretion rates of cool, old white dwarfs over Gyr time-scales. Here, we revisit those results using updated white dwarf models and larger samples of old polluted H- and He-atmosphere white dwarfs. We find no compelling evidence for a strong decrease of their time-averaged mass accretion rates for cooling times between 1 and 8 Gyr. Over this period, the mass accretion rates decrease by no more than a factor of the order of 10, which is one order of magnitude smaller than the decay rate found in recent works. Our results require mechanisms that can efficiently and consistently deliver planetesimals inside the Roche radius of white dwarfs over at least 8 Gyr.
Constraining the evolution of cataclysmic variables via the masses and accretion rates of their underlying white dwarfs
Authors: Pala A F , Gänsicke B T , Belloni D , Parsons S G , Marsh T R , Schreiber M R , Breedt E , Knigge C , Sion E M , Szkody P , Townsley D , Bildsten L , Boyd D , Cook M J , De Martino D , Godon P , Kafka S , Kouprianov V , Long K S , Monard B , Myers G , Nelson P , Nogami D , Oksanen A , Pickard R , Poyner G , Reichart D E , Rodriguez Perez D , Shears J , Stubbings R , Toloza O
Published: November 2021

We report on the masses (MWD), effective temperatures ($\rm{T_\mathrm{eff}}$), and secular mean accretion rates ($\langle \dot{M} \rangle$) of 43 cataclysmic variable (CV) white dwarfs, 42 of which were obtained from the combined analysis of their Hubble Space Telescope ultraviolet data with the parallaxes provided by the Early Third Data Release of the Gaia space mission, and one from the white dwarf gravitational redshift. Our results double the number of CV white dwarfs with an accurate mass measurement, bringing the total census to 89 systems. From the study of the mass distribution, we derive $\langle M_\mathrm{WD} \rangle = 0.81^{+0.16}_{-0.20}\, \mathrm{M_\odot }$, in perfect agreement with previous results, and find no evidence of any evolution of the mass with orbital period. Moreover, we identify five systems with MWD < 0.5 M⊙, which are most likely representative of helium-core white dwarfs, showing that these CVs are present in the overall population. We reveal the presence of an anticorrelation between the average accretion rates and the white dwarf masses for the systems below the $2\!-\!3\,$ h period gap. Since $\langle \dot{M} \rangle$ reflects the rate of system angular momentum loss, this correlation suggests the presence of an additional mechanism of angular momentum loss that is more efficient at low white dwarf masses. This is the fundamental concept of the recently proposed empirical prescription of consequential angular momentum loss (eCAML) and our results provide observational support for it, although we also highlight how its current recipe needs to be refined to better reproduce the observed scatter in $\rm{T_\mathrm{eff}}$ and $\langle \dot{M} \rangle$, and the presence of helium-core white dwarfs.
Structure, dynamics, and function of SrnR, a transcription factor for nickel-dependent gene expression
Authors: Mazzei Luca , Musiani Francesco , Żerko Szymon , Koźminski Wiktor , Cianci Michele , Beniamino Ylenia , Ciurli Stefano , Zambelli Barbara
Published: November 2021

Streptomyces griseus, a bacterium producing antibacterial drugs and featuring possible application in phytoremediation, expresses two metal-dependent superoxide dismutase (SOD) enzymes, containing either Fe(II) or Ni(II) in their active site. In particular, the alternative expression of the two proteins occurs in a metal-dependent mode, with the Fe(II)-enzyme gene (sodF) repressed at high intracellular Ni(II) concentrations by a two-component system (TCS). This complex involves two proteins, namely SgSrnR and SgSrnQ, which represent the transcriptional regulator and the Ni(II) sensor of the system, respectively. SgSrnR belongs to the ArsR/SmtB family of metal-dependent transcription factors; in the apo-form and in the absence of SgSrnQ, it can bind the DNA operator of sodF, upregulating gene transcription. According to a recently proposed hypothesis, Ni(II) binding to SgSrnQ would promote its interaction with SgSrnR, causing the release of the complex from DNA and the consequent downregulation of the sodF expression. SgSrnQ is predicted to be highly disordered, thus the understanding, at the molecular level, of how the SgSrnR/SgSrnQ TCS specifically responds to Ni(II) requires the knowledge of the structural, dynamic, and functional features of SgSrnR. These were investigated synergistically in this work using X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, atomistic molecular dynamics calculations, isothermal titration calorimetry, and in silico molecular docking. The results reveal that the homodimeric apo-SgSrnR binds to its operator in a two-step process that involves the more rigid globular portion of the protein and leaves its largely disordered regions available to possibly interact with the disordered SgSrnQ in a Ni-dependent process.
A simple and general approach to generate photoactivatable DNA processing enzymes
Authors: Kesici Merve-Zeynep , Tinnefeld Philip , Vera Andrés Manuel
Published: November 2021

DNA processing enzymes, such as DNA polymerases and endonucleases, have found many applications in biotechnology, molecular diagnostics, and synthetic biology, among others. The development of enzymes with controllable activity, such as hot-start or light-activatable versions, has boosted their applications and improved the sensitivity and specificity of the existing ones. However, current approaches to produce controllable enzymes are experimentally demanding to develop and case-specific. Here, we introduce a simple and general method to design light-start DNA processing enzymes. In order to prove its versatility, we applied our method to three DNA polymerases commonly used in biotechnology, including the Phi29 (mesophilic), Taq, and Pfu polymerases, and one restriction enzyme. Light-start enzymes showed suppressed polymerase, exonuclease, and endonuclease activity until they were re-activated by an UV pulse. Finally, we applied our enzymes to common molecular biology assays and showed comparable performance to commercial hot-start enzymes.
Efficacy and safety of larotrectinib in TRK fusion-positive primary central nervous system tumors
Authors: Doz François , van Tilburg Cornelis M , Geoerger Birgit , Højgaard Martin , Øra Ingrid , Boni Valentina , Capra Michael , Chisholm Julia , Chung Hyun Cheol , DuBois Steven G , Gallego-Melcon Soledad , Gerber Nicolas U , Goto Hiroaki , Grilley-Olson Juneko E , Hansford Jordan R , Hong David S , Italiano Antoine , Kang Hyoung Jin , Nysom Karsten , Thorwarth Anne , Stefanowicz Joanna , Tahara Makoto , Ziegler David S , Gavrilovic Igor T , Norenberg Ricarda , Dima Laura , De La Cuesta Esther , Laetsch Theodore W , Drilon Alexander , Perreault Sebastien
Published: November 2021

Background

Larotrectinib is a first-in-class, highly selective tropomyosin receptor kinase (TRK) inhibitor approved to treat adult and pediatric patients with TRK fusion-positive cancer. The aim of this study was to evaluate the efficacy and safety of larotrectinib in patients with TRK fusion-positive primary central nervous system (CNS) tumors.

Methods

Patients with TRK fusion-positive primary CNS tumors from two clinical trials (NCT02637687, NCT02576431) were identified. The primary endpoint was investigator-assessed objective response rate (ORR).

Results

As of July 2020, 33 patients with TRK fusion-positive CNS tumors were identified (median age: 8.9 years; range: 1.3–79.0). The most common histologies were high-grade glioma (HGG; n = 19) and low-grade glioma (LGG; n = 8). ORR was 30% (95% confidence interval [CI]: 16–49) for all patients. The 24-week disease control rate was 73% (95% CI: 54–87). Twenty-three of 28 patients (82%) with measurable disease had tumor shrinkage. The 12-month rates for duration of response, progression-free survival, and overall survival were 75% (95% CI: 45–100), 56% (95% CI: 38–74), and 85% (95% CI: 71–99), respectively. Median time to response was 1.9 months (range 1.0–3.8 months). Duration of treatment ranged from 1.2–31.3+ months. Treatment-related adverse events were reported for 20 patients, with grade 3–4 in 3 patients. No new safety signals were identified.

Conclusions

In patients with TRK fusion-positive CNS tumors, larotrectinib demonstrated rapid and durable responses, high disease control rate, and a favorable safety profile.
The Ethics of Selective Mandatory Vaccination for COVID-19
Authors: Williams Bridget M
Published: November 2021

With evidence of vaccine hesitancy in several jurisdictions, the option of making COVID-19 vaccination mandatory requires consideration. In this paper I argue that it would be ethical to make the COVID-19 vaccination mandatory for older people who are at highest risk of severe disease, but if this were to occur, and while there is limited knowledge of the disease and vaccines, there are not likely to be sufficient grounds to mandate vaccination for those at lower risk. Mandating vaccination for those at high risk of severe disease is justified on the basis of the harm principle, as there is evidence that this would remove the grave public health threat of COVID-19. The risk–benefit profile of vaccination is also more clearly in the interests of those at highest risk, so mandatory vaccination entails a less severe cost to them. Therefore, a selective mandate would create fairness in the distribution of risks. The level of coercion imposed by a mandate would need to be proportionate, and it is likely that multiple approaches will be needed to increase vaccine uptake. However, a selective mandate for COVID-19 vaccines is likely to be an ethical choice and should be considered by policy-makers.
Peripheral manifestations are major determinants of disease phenotype and outcome in new onset spondyloarthritis
Authors: De Craemer Ann-Sophie , Renson Thomas , Deroo Liselotte , Van Praet Liesbet , Cypers Heleen , Varkas Gaëlle , Joos Rik , Devinck Mieke , Gyselbrecht Lieve , Peene Isabelle , Thevissen Kristof , Costantino Félicie , D’Agostino Maria-Antonietta , Lenaerts Jan , Carron Philippe , Van den Bosch Filip , Elewaut Dirk
Published: November 2021

Objectives

To delineate the impact of peripheral musculoskeletal manifestations on stratification of disease phenotype and outcome in new-onset spondyloarthritis (SpA), using a prospective observational nationwide inception cohort, the BelGian Inflammatory Arthritis and spoNdylitis cohorT (Be-Giant).

Methods

Newly diagnosed adult SpA patients, fulfilling the Assessment of SpondyloArthritis International Society (ASAS) criteria for axial or peripheral SpA, were included in Be-Giant and prospectively followed every six months. Peripheral involvement (defined as arthritis, enthesitis and/or dactylitis) was determined in relation to clinically similar patient subsets at baseline and disease activity patterns during two-year follow-up, identified through K-means cluster analysis and latent class growth analysis.

Results

From November 2010 to March 2020, 367 patients were enrolled in Be-Giant, of whom 162 (44%) had peripheral manifestations. Two patient clusters [A, axial predominant (n = 248) and B, peripheral predominant (n = 119)] were identified at diagnosis. Longitudinal analysis (n = 115) revealed two trajectories of disease activity in each cluster: one with persistently high disease activity over time (‘High’), the other rapidly evolving to low disease activity (‘Low’). In cluster A patients, peripheral manifestations predisposed to the ‘High’ trajectory [odds ratio (OR) = 2.0, 95% CI: 1.3, 3.1, P = 0.001], despite more rapid initiation of biologics compared with patients without peripheral manifestations (hazard ratio (HR)  = 2.1, 95% CI: 1.0, 4.4, P = 0.04 – Cox proportional-hazards model).

Conclusion

Peripheral musculoskeletal manifestations are major determinants of phenotypical diversity in new-onset SpA. Intriguingly, stratification of axial SpA according to concomitant peripheral involvement identified an endotype with an unfavorable outcome despite more prompt therapeutic intensification with biologics. These observations justify an endotype-tailored approach beyond current ASAS/EULAR management recommendations.
How Important Is Temptation Spending? Maybe Less than We Thought
Authors: Brune Lasse , Kerwin Jason T , Li Qingxiao
Published: November 2021

Temptation plays a key role in theoretical work on spending and saving in developing countries. The limited empirical evidence on its importance, however, suggests that cash transfers do not induce increases in temptation spending. This paper expands the evidence base by studying the effect of randomized exposure to temptation on spending decisions in rural Malawi. Consistent with the cash transfer literature, a more tempting environment does not induce significant changes in temptation spending. However, the magnitudes of both temptation spending levels and the treatment effects are somewhat sensitive to the definition of temptation spending used. This paper examines the potential factors that may be driving these null results, and suggests that future research may find a limited role for temptation in the economic decisions of the poor.
Sweetpotato Genotypes ‘CIP BRS Nuti’ and ‘Canadense’ Are Resistant toMeloidogyne incognita,M.javanica, andM.enterolobii
Authors: Mello Alexandre F. S. , Silva Gabriela , de Sousa Raquel L. , Barbosa Alexandre V. S. , Nakasu Erich Y. T. , Silva Giovani O. , Biscaia Danielle , Pinheiro Jadir B.
Published: November 2021

Sweetpotato is a staple crop in Brazil presenting a smaller number of pathogens and diseases in comparison with other root and tuberous crops. Root-knot nematodes are among the most serious sweetpotato root pathogens. The impact of these pathogens also extends to succeeding crops. Because in Brazil, it is common to cultivate more than one crop per season, this problem is rapidly disseminated. The aim of this study was to assess the resistance of two sweetpotato clones and four commercial sweetpotato genotypes to three different Meloidogyne species. Assays were performed under greenhouse and field conditions. ‘CIP BRS Nuti’ and ‘Canadense’ were resistant to Meloidogyne incognita, M. javanica, and M. enterolobii under greenhouse conditions. This finding was obtained based on the reproduction factor < 0.2, meaning that the initial population of 5,000 nematodes was reduced to <1,000 individuals after 90 days of inoculation. Tomato and sweetpotato cultivar Beauregard, known to be susceptible to the three nematode species, were highly damaged by the pathogens. Similar results were also observed under field conditions. To our knowledge, ‘CIP BRS Nuti’ and ‘Canadense’ are the first South American commercial cultivars with triple nematode resistance.
Identification and Mapping of QTL for Stripe Rust Resistance in the Chinese Wheat Cultivar Shumai126
Authors: Wang Yufan , Hu Yanling , Gong Fangyi , Jin Yarong , Xia Yingjie , He Yu , Jiang Yun , Zhou Qiang , He Jingshu , Feng Lihua , Chen Guoyue , Zheng Youliang , Liu Dengcai , Huang Lin , Wu Bihua
Published: November 2021

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a damaging disease of wheat globally, and breeding resistant cultivars is the best control strategy. The Chinese winter wheat cultivar Shumai126 (SM126) exhibited strong resistance to P. striiformis f. sp. tritici in the field for more than 10 years. The objective of this study was to identify and map quantitative trait loci (QTL) for resistance to stripe rust in a population of 154 recombinant inbred lines (RILs) derived from a cross between cultivars Taichang29 (TC29) and SM126. The RILs were tested in six field environments with a mixture of the Chinese prevalent races (CYR32, CYR33, CYR34, Zhong4, and HY46) of P. striiformis f. sp. tritici and in growth chamber with race CYR34 and genotyped using the Wheat55K single nucleotide polymorphism (SNP) array. Six QTL were mapped on chromosomes 1BL, 2AS, 2AL, 6AS, 6BS, and 7BL, respectively. All QTL were contributed by SM126 except QYr.sicau-2AL. The QYr.sicau-1BL and QYr.sicau-2AS had major effects, explaining 27.00 to 39.91% and 11.89 to 17.11% of phenotypic variances, which may correspond to known resistance genes Yr29 and Yr69, respectively. The QYr.sicau-2AL, QYr.sicau-6AS, and QYr.sicau-6BS with minor effects are likely novel. QYr.sicau-7BL was only detected based on growth chamber seedling data. Additive effects were detected for the combination of QYr.sicau-1BL, QYr.sicau-2AS, and QYr.sicau-2AL. SNP markers linked to QYr.sicau-1BL (AX-111056129 and AX-108839316) and QYr.sicau-2AS (AX-111557864 and AX-110433540) were converted to breeder-friendly Kompetitive allele-specific PCR (KASP) markers that would facilitate the deployment of stripe rust resistance genes in wheat breeding.
Identification and Genetic Characterization ofPseudomonas syringaepv. syringaefrom Sweet Cherry in Turkey
Authors: Oksel Cansu , Avin Farhat A. , Mirik Mustafa , Baysal-Gurel Fulya
Published: November 2021

Pseudomonas syringae pv. syringae, which causes bacterial canker, is the most polyphagous bacterium in the P. syringae complex because of its broad host range. This pathogen is considered the major bacterial disease in cherry orchards. In this study, several samples were collected from infected sweet cherry (Prunus avium L.) trees in different locations of the Marmara region in Turkey between 2016 and 2018. Sixty-three isolates were identified as P. syringae pv. syringae by pathogenicity, LOPAT, GATTa, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry tests. Total genomic DNA was extracted to confirm identity, followed by PCR amplification of syrB and cfl genes. Out of 63 isolates, 12 were randomly selected for repetitive element sequence-based PCR and multilocus sequence typing analyses to gain insight into the relationships of those isolates. The cluster analysis of enterobacterial repetitive intergenic consensus-, repetitive extragenic palindromic-, and BOX-A1R-based repetitive extragenic-palindromic-PCR techniques could classify the isolates into two distinct clusters. Phylogenetic analysis was carried out to obtain the relation between isolates and the location. The multilocus sequencing typing analysis of gyrB, rpoDp, rpoDs, and gltA genes allowed a clear allocation of the isolates into two separate main clusters. The relationships among the isolates were also evaluated by constructing a genealogical median-joining network (MJN). The isolates from six locations produced 11 haplotypes that were illustrated in the MJN. The results of this study proved that location could not be an indicator for showing the genetic diversity of P. syringae pv. syringae from cherry orchards. As the genetic variability of Pseudomonads has been demonstrated, this study also showed high diversity among different isolates even within the populations. While more research is recommended, the results of this study contributed to a better understanding of the evolutionary progress of P. syringae pv. syringae and the genetic diversity of sweet cherry isolates.
Diversity of Fusarium spp. Associated with Wheat Node and Grain in Representative Sites Across the Western Canadian Prairies
Authors: Hafez Mohamed , Gourlie Ryan , Telfer Melissa , Schatz Nicola , Turkington Thomas K. , Beres Brian , Aboukhaddour Reem
Published: November 2021

Fusarium head blight (FHB) and Fusarium crown and root rot (FCRR) are major wheat diseases. Populations of FHB and FCRR pathogens are highly dynamic, and shifts in these populations in different regions is reported. Analyzing fungal populations associated with wheat node and grain tissues collected from different regions can provide useful information and predict diseases that might affect subsequent crops and effective disease management practices. In this study, wheat node and grain samples were collected from four representative sites across the western Canadian prairies in the 2018 growing season to characterize the major Fusarium spp. and other mycobiota associated with wheat in these regions. In total, 994 fungal isolates were recovered, and based on culture and molecular diagnostic methods, three genera constituted over 90% of all fungal isolates, namely Alternaria (39.6%), Fusarium (27.8%), and Parastagonospora (23.9%). A quantitative PCR (qPCR) diagnostic toolkit was developed to quantify the most frequently isolated Fusarium spp. in infected wheat tissues: Fusarium avenaceum, F. culmorum, F. graminearum, and F. poae. This qPCR specificity was validated in silico, in vitro, and in planta and proved specific to the target species. The qPCR results showed that F. graminearum was not detected frequently from wheat node and grain samples collected from four locations in this study. F. poae was the most abundant Fusarium species in grain samples in all tested locations. However, in node samples, F. culmorum (Beaverlodge and Scott) and F. avenaceum (Lacombe and Lethbridge) were the most abundant species. Trichothecene genotyping showed that the 3ADON is the most dominant trichothecene genotype (68%), followed by type-A trichothecenes (29.5%), whereas the 15ADON trichothecene genotype was least dominant (2.5%) and the NIV genotype was not detected. Moreover, a total of 129 translation elongation factor 1-alpha (TEF1α) sequences from nine Fusarium spp. were compared at the haplotype level to evaluate genetic variability and distribution. F. avenaceum and F. poae exhibited higher diversity as reflected by higher number of haplotypes present in these two species compared with the rest.
Nurses' House—for Nurses
Authors: Todd Betsy
Published: November 2021

Editor's note: From its first issue in 1900 through to the present day, AJN has unparalleled archives detailing nurses' work and lives over more than a century. These articles not only chronicle nursing's growth as a profession within the context of the events of the day, but also reveal prevailing societal attitudes about women, health care, and human rights. Today's nursing school curricula rarely include nursing's history, but it's a history worth knowing. To this end, From the AJN Archives highlights articles selected to fit today's topics and times.

This month's article, from January 1939, describes Nurses' House in Long Island, New York, where nurses could stay for “fun or rest, or just plain comfort and content.” The home was a legacy of Emily H. Bourne, who was known primarily for her support of the blind and for building what is now the New Bedford Whaling Museum in Massachusetts. Bourne (who was not a nurse) left money in her will for the purchase of a mansion where nurses could come to rest and relax between cases.

The home was sold in 1959 to create a fund for nurses in need. Today, Nurses' House is a nonprofit, nurse-managed, national service organization that provides short-term financial assistance to nurses in all 50 states. For more on nurses' well-being—especially relevant amid a global pandemic—see this month's original research article, “Well-Being and Resilience Among Health Care Workers During the COVID-19 Pandemic: A Cross-Sectional Study.”—Betsy Todd, MPH, RN
Secondary Medication Administration and IV Smart Pump Setup
Authors: Giuliano Karen K. , Blake Jeannine W. C. , Butterfield Robert
Published: November 2021

Secondary infusion by large-volume IV smart pump is used extensively in the acute care setting for one-time or intermittent administration of medications such as antibiotics, electrolyte replacements, and some oncology drugs. Consistent and accurate delivery of secondary medications requires a full understanding of the system and setup requirements. Unfortunately, it is not uncommon for nurses to find a secondary medication only partially administered when their programming should have resulted in a complete infusion. This article discusses the technical requirements that every nurse should know when administering secondary medications using an IV smart pump.
High-Flow Nasal Oxygen vs. Noninvasive Ventilation or Conventional Oxygen Therapy in Acute Respiratory Failure
Authors: Rosenberg Karen
Published: November 2021

According to this study:

Compared with noninvasive ventilation, high-flow nasal oxygen used in the initial management of acute respiratory failure may improve several clinical outcomes.

Compared with conventional oxygen therapy, high-flow nasal oxygen used in postextubation management may reduce reintubations and improve patient comfort.
Second Primary Malignancies in Chronic Lymphocytic Leukaemia; Skin, Solid Organ, Haematological, and Richter’s Syndrome
Authors: Shen Yandong , Coyle Luke , Kerridge Ian , Stevenson William , Arthur Christopher , McKinlay Naomi , Fay Keith , Ward Christopher , Greenwood Matthew , Best O. Giles , Solterbeck Ann , Guminski Alexander , Shumack Stephen , Mulligan Stephen P.
Published: November 2021

Chronic lymphocytic leukaemia (CLL) is invariably accompanied by some degree of immune failure. CLL patients have a high rate of second primary malignancy (SPM) compared to the general population. We comprehensively documented the incidence of all forms of SPM including skin cancer (SC), solid organ malignancy (SOM), second haematological malignancy (SHM), and separately Richter’s Syndrome (RS) across all therapy eras. Among the 517 CLL/SLL patients, the overall incidence of SPMs with competing risks were SC 31.07%, SOM 25.99%, SHM 5.19% and RS 7.55%. Melanoma accounted for 30.3% of SC. Squamous cell carcinoma (SCC), including 8 metastatic SCCs, was 1.8 times more than basal cell carcinoma (BCC), a reversal of the typical BCC:SCC ratio. The most common SOM were prostate (6.4%) and breast (4.5%). SHM included 7 acute myeloid leukaemia and 5 myelodysplasia of which 8 were therapy-related. SPMs are a major health burden with 44.9% of CLL patients with at least one, and apart from SC, associated with significantly reduced overall survival. Dramatic improvements in CLL treatment and survival have occurred with immunochemotherapy and targeted therapies but mitigating SPM burden will be important to sustain further progress.
Reinfection with SARS-CoV-2: outcome, risk factors and vaccine efficacy in a Scottish cohort
Authors: McKeigue Paul M , McAllister David A , Robertson Chris , Stockton Diane , Colhoun Helen M ,   for the PHS COVID-19 Epidemiology and Research Cell
Published: November 2021

Background

The objective of this study was to investigate how protection against COVID-19 conferred by previous infection is modified by vaccination.

Methods

In a cohort of all 152655 individuals in Scotland alive at 90 days after a positive test for SARS-CoV-2 (confirmed by cycle threshold < 30, or two tests) followed till 22 September 2021, rate ratios for reinfection were estimated with calendar time or tests as timescale.

Findings

Rates of detected and hospitalised reinfection with COVID-19 while unvaccinated were respectively 6.8 (95% CI 6.4 to 7.2) and 0.18 (95% CI 0.12 to 0.25) per 1000 person-months. These rates were respectively 68% and 74% lower than in a matched cohort of individuals who had not previously tested positive. Efficacy of two doses of vaccine in those with previous infection was estimated as as 84% (95 percent CI 81% to 86%) against detected reinfection and 71% (95 percent CI 29% to 88%) against hospitalised or fatal reinfection. The rate of detected reinfection after two doses of vaccine was 1.35 (95% CI 1.02 to 1.78) times higher in those vaccinated before first infection than in those unvaccinated at first infection.

Interpretation

The combination of natural infection and vaccination provides maximal protection against new infection with SARS-CoV-2: prior vaccination does not impair this protection.

Funding

No specific funding was received for this work.

Research in context

Evidence before this study

In a recent systematic review of cohort studies reported up to July 2021, the average reduction in COVID-19 infection rates in those with previous infection compared with those without evidence of previous infection was 90%. There is little information about the protective effect of previous infection against severe COVID-19, or about how the protective effects of previous infection against reinfection and severe disease are modified by vaccination.

What this paper adds

In unvaccinated individuals the protection against hospitalised COVID-19 conferred by previous infection is similar to that induced by vaccination. In those with previous infection, vaccination reduces the rates of reinfection and hospitalised COVID-19 by about 70%.

Implications of all the available evidence

The combination of natural infection and vaccination provides maximal protection against COVID-19: prior vaccination does not seriously impair this protection.
Vaccination strategies in structured populations under partial immunity and reinfection
Authors: Rodriguez-Maroto Gabriel , Atienza-Diez Iker , Ares Saúl , Manrubia Susanna
Published: November 2021

Optimal protocols of vaccine administration to minimize the effects of infectious diseases depend on a number of variables that admit different degrees of control. Examples include the characteristics of the disease and how it impacts on different groups of individuals as a function of sex, age or socioeconomic status, its transmission mode, or the demographic structure of the affected population. Here we introduce a compartmental model of infection propagation with vaccination and reinfection and analyse the effect that variations on the rates of these two processes have on the progression of the disease and on the number of fatalities. The population is split into two groups to highlight the overall effects on disease caused by different relationships between vaccine administration and various demographic structures. We show that optimal administration protocols depend on the vaccination rate, a variable severely conditioned by vaccine supply and acceptance. As a practical example, we study COVID-19 dynamics in various countries using real demographic data. The model can be easily applied to any other disease and demographic structure through a suitable estimation of parameter values. Simulations of the general model can be carried out at this interactive webpage [1].

Author summary

Vaccination campaigns can have varying degrees of success in minimizing the effects of an infectious disease. It is often very difficult to assess a priori the importance and effect of different relevant factors. To gain insight into this problem, we present a model of infection propagation with vaccination and use it to study the effects of vaccination rate and population structure. We find that when the disease affects in different ways distinct population groups, the best vaccination strategy depends non-trivially on the rate at which vaccines can be administered. The application of our analysis to COVID-19 reveals that, in countries with aged populations, the best strategy is always to vaccinate first the elderly, while for youthful populations maximizing vaccination rate regardless of other considerations may save more lives.
SARS-CoV-2 within-host and in-vitro genomic variability and sub-genomic RNA levels indicate differences in viral expression between clinical and in-vitro cohorts
Authors: Agius Jessica E. , Johnson-Mackinnon Jessica C. , Fong Winkie , Gall Mailie , Lam Connie , Basile Kerri M. , Kok Jen , Arnott Alicia , Sintchenko Vitali , Rockett Rebecca J.
Published: November 2021

Background

Low frequency intrahost single nucleotide variants (iSNVs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have been increasingly recognised as predictive indicators of positive selection. Particularly as growing numbers of SARS-CoV-2 variants of interest (VOI) and concern (VOC) emerge. However, the dynamics of subgenomic RNA (sgRNA) expression and its impact on genomic diversity and infection outcome remain poorly understood. This study aims to investigate and quantify iSNVs and sgRNA expression in single and longitudinally sampled cohorts over the course of mild and severe SARS-CoV-2 infection benchmarked against an in-vitro infection model.

Methods

Two clinical cohorts of SARS-CoV-2 positive cases in New South Wales, Australia collected between March 2020 and August 2021 were sequenced. Longitudinal samples from cases hospitalised due to SARS-CoV-2 infection (severe) were analysed and compared with cases that presented with SARS-CoV-2 symptoms but were not hospitalised (mild). SARS-CoV-2 genomic diversity profiles were also examined from daily sampling of culture experiments for three SARS-CoV-2 variants (Lineage A, B.1.351, and B.1.617.2) cultured in VeroE6 C1008 cells (n = 33).

Results

ISNVs were detected in 83% (19/23) of the mild cohort cases and 100% (16/16) of the severe cohort cases. SNP profiles remained relatively fixed over time, with an average of 1.66 SNPs gained or lost and an average of 4.2 and 5.9 low frequency variants per patient were detected in severe and mild infection, respectively. SgRNA was detected in 100% (25/25) of the mild genomes and 92% (24/26) of the severe genomes. Total sgRNA expressed across all genes in the mild cohort was significantly higher than that of the severe cohort. Significantly higher expression levels were detected in the spike and the nucleocapsid genes. There was significantly less sgRNA detected in the culture cohort than the clinical.

Discussion and Conclusions

The positions and frequencies of iSNVs in the severe and mild infection cohorts were dynamic overtime, highlighting the importance of continual monitoring, particularly during community outbreaks where multiple SARS-Cov-2 variants may co-circulate. SgRNA levels can vary across patients and the overall level of sgRNA reads compared to genomic RNA can be less than 1%. The relative contribution of sgRNA to the severity of illness warrants further investigation given the level of variation between genomes. Further monitoring of sgRNAs will improve the understanding of SARS-CoV-2 evolution and the effectiveness of therapeutic and public health containment measures during the pandemic.
Characterization of the immune resistance of SARS-CoV-2 Mu variant and the immunity induced by Mu infection
Authors: Uriu Keiya , Cárdenas Paúl , Muñoz Erika , Barragan Veronica , Kosugi Yusuke , Shirakawa Kotaro , Takaori-Kondo Akifumi ,   Ecuador-COVID19 Consortium,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato Kei
Published: November 2021

We have revealed that the SARS-CoV-2 Mu variant is highly resistant to COVID-19 convalescent sera and vaccine sera.1 However, it remains unclear how the immune resistance of the Mu variant is determined. Also, although the Mu variant is highly resistant to the sera obtained from COVID-19 convalescent during early pandemic (i.e., infected with prototypic virus) and vaccinated individuals (i.e., immunized based on prototypic virus), it was unaddressed how the convalescent sera from Mu-infected individuals function. In this study, we revealed that the two mutations in the spike protein of Mu variant, YY144-145TSN and E484K, are responsible for the potent immune resistance of Mu variant. Additionally, we showed that the convalescent sera obtained from the Mu-infected individuals can be broadly antiviral against the Mu variant as well as other SARS-CoV-2 variants of concern/interest. Our findings suggest that developing novel vaccines based on the Mu variant can be more effective against a broad range of SARS-CoV-2 variants.
Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission: a prospective cohort study in England
Authors: Clifford Samuel , Waight Pauline , Hackman Jada , Hué Stephane , Gower Charlotte M , Kirsebom Freja CM , Skarnes Catriona , Letley Louise , Bernal Jamie Lopez , Andrews Nick , Flasche Stefan , Miller Elizabeth
Published: November 2021

Background

The ability of SARS-CoV-2 vaccines to protect against infection and onward transmission determines whether immunisation can control global circulation. We estimated effectiveness of BNT162b2 and ChAdOx1 vaccines against acquisition and transmission of the Alpha and Delta variants in a prospective household study in England.

Methods

Adult index cases in the community and their household contacts took oral-nasal swabs on days 1, 3 and 7 after enrolment. Swabs were tested by RT-qPCR with genomic sequencing conducted on a subset. We used Bayesian logistic regression to infer vaccine effectiveness against acquisition and transmission, adjusted for age, vaccination history and variant.

Findings

Between 2 February 2021 and 10 September 2021 213 index cases and 312 contacts were followed up. After excluding households lacking genomic proximity (N=2) or with unlikely serial intervals (N=16), 195 households with 278 contacts remained of whom 113 (41%) became PCR positive. Delta lineages had 1.64 times the risk (95% Credible Interval: 1.15 – 2.44) of transmission than Alpha; contacts older than 18 years were 1.19 times (1.04 - 1.52) more likely to acquire infection than children. Effectiveness of two doses of BNT162b2 against transmission of Delta was 31% (−3%, 61%) and 42% (14%, 69%) for ChAdOx1, similar to their effectiveness for Alpha. Protection against infection with Alpha was higher than for Delta, 71% (12%,95%) vs 24% (−2%, 64%) respectively for BNT162b2 and 26% (−39%, 73%) vs 14% (−5%, 46%) respectively for ChAdOx1.

Interpretation

BNT162b2 and ChAdOx1 reduce transmission of the Delta variant from breakthrough infections in the household setting though their protection against infection is low.

Funding

This study was funded by the UK Health Security Agency (formerly Public Health England) as part of the COVID-19 response.
Uptake of Covid-19 preventive measures among 10 immigrant ethnic groups in Norway
Authors: Gele Abdi , Sheikh Naima Said , Kour Prabhjot , Qureshi Samera A
Published: November 2021

Background

A pessimistic view of the impact of Covid-19 on immigrants has generated an interest in exploring the role of socio-economic and cultural factors on excess infection, hospitalization and death among immigrants. Nowhere in the world is such interest more palpable than in Western countries, including Norway. An expanding amount of literature has demonstrated that preexisting socio-economic inequalities have affected Covid-19 control programs through a disruption of immigrants’ uptake to preventive measures. Nonetheless, until very recently, no qualitative research has been conducted to address the impact of socio-economic and socio-cultural factors on immigrants’ uptake on preventive measures of Covid-19 in Norway.

Methods

An interview-based qualitative study consisting of 88 participants (49 women and 39 men) from 10 immigrant ethnic groups were carried out. Participants were recruited through purposive sampling and snowballing. In-depth interviews were held through telephone or online for those who have experience in the use of zoom or teams. Data were analyzed using thematic analysis

Results

We found that participants’ attitudes toward the pandemic in general, and more specifically their adherence to preventive measures, have increased over time. However, the number of barriers that hinder immigrants from adhering to preventive measures were identified and classified more broadly into three main subthemes: 1) socio-economic barriers; 2) socio-cultural barriers, and 3) other barriers. Socio-economic barriers include overcrowded households, working in first-line jobs, education and language. Socio-cultural barriers include collectivist culture, religious fatalism and risk perception toward the pandemic.

Conclusion

To reduce the health inequality that arises from overcrowded housing, there is a need for a long-term strategy to help improve the housing situation of low-income immigrant families that live in overcrowded households. In addition, increasing health literacy and more generally, the integration of immigrants, may also reduce the effect of socio-cultural factors on an immigrant’s uptake of preventive measures.
The Understanding persistent Pain Where it ResiDes study of low back pain cohort profile
Authors: Jenkins Luke C , Chang Wei-Ju , Buscemi Valentina , Liston Matthew , Nicholas Michael , Graven-Nielsen Thomas , Hodges Paul W , Wasinger Valerie C , Stone Laura S , Dorsey Susan G , McAuley James H , Schabrun Siobhan M
Published: November 2021

Background

Despite chronic low back pain (LBP) being considered a biopsychosocial condition for diagnosis and management, few studies have investigated neurophysiological or neurobiological risk factors thought to underpin the transition from acute to chronic LBP. The aim of this cohort profile is to describe the methodology, compare baseline characteristics between acute LBP participants and pain-free controls, and compare LBP participants with or without completed follow-up.

Methods

120 individuals experiencing acute LBP and 57 pain-free controls were recruited to participate in the Understanding Persistent Pain Where it Resides (UPWaRD) study. Screening was conducted via email and phone. Neurobiological, psychological, and sociodemographic data were collected at baseline, three- and six-months. LBP status was assessed using the numerical rating scale and Roland-Morris disability questionnaire at three and six-month follow-up.

Results

95 participants (79%) provided outcome data at three-month follow-up and 96 participants (80%) at six-months. Participants who did not complete follow-up at three- and six-months within the UPWaRD LBP cohort had higher psychological distress, higher pain interference, higher levels of moderate physical activity, and reported occupational difficulties due to pain (P = <0.05). Compared to controls, LBP participants in the UPWaRD cohort were older, had a higher BMI, a higher prevalence of comorbidities and higher medication usage. Higher depression, anxiety and stress, lower pain self-efficacy and higher pain catastrophizing during acute LBP were correlated with higher six-month pain and disability (P = < 0.01).

Conclusions

This cohort profile reports baseline characteristics of the UPWaRD LBP and pain-free control cohort.