bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Ce(NO3)3 concentration on microstructure and properties of plasma electrolytic oxidation layer on 6061 alloy
Authors: Shang Jian , Liu Fu , Gu Gaoyang , Meng Lingyao
Published: July 2022

Plasma electrolytic oxidation treatment of 6061 Al alloy was carried out in a sodium silicate and sodium hydroxide alkaline electrolyte containing different concentrations of cerium nitrate (Ce (NO3)3) under constant current mode. The effects of Ce (NO3)3 concentration on the roughness, cross section and surface morphology, composition and phase composition, adhesion force and corrosion resistance of the prepared layer were studied by means of true color microscope, scanning electron microscope, x-ray energy spectrometer, x-ray diffractometer, micrometer scratcher and electrochemical workstation. The results show that with the increase of Ce(NO3)3 concentration in the electrolyte, the thickness of the plasma electrolytic oxidation layer increases gradually, and the micropores and cracks increase, and the roughness increases first and then decreases. The plasma electrolytic oxidation layers under different concentrations of Ce (NO3)3 are mainly composed of α-Al2O3, γ-Al2O3 and a small amount of Al2SiO5. The Ce element in the layer is mainly present in the form of a mixture of Ce(OH)4, CeO2 and Ce2O3.The increase of Ce (NO3)3 concentration reduces the binding strength between the plasma electrolytic oxidation layer and the matrix, increases the self-corrosion potential, decreases the self-corrosion current, and weakens the corrosion resistance. The layer with a concentration of 0.25 g l−1 Ce (NO3)3 has less micropores and cracks, and has the better compactness. The bonding strength between the layer and the substrate is 27 N, the corrosion current density is 3.42 × 10−9A cm−2 and corrosion potential is −0.72 V, the best bonding strength and corrosion resistance is presented.
Local well-posedness for quasi-linear problems: A primer
Authors: Ifrim Mihaela , Tataru Daniel
Published: July 2022

Proving local well-posedness for quasi-linear problems in partial differential equations presents a number of difficulties, some of which are universal and others of which are more problem specific. On one hand, a common standard for what well-posedness should mean has existed for a long time, going back to Hadamard. On the other hand, in terms of getting there, there are by now both many variations—and also many misconceptions.

The aim of these expository notes is to collect a number of both classical and more recent ideas in this direction, and to assemble them into a cohesive roadmap that can be then adapted to the reader’s problem of choice.
Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications
Authors: Gómez-González Paula J , Campino Susana , Phelan Jody E , Clark Taane G
Published: July 2022

With >1 million associated deaths in 2020, human tuberculosis (TB) caused by the bacteria Mycobacterium tuberculosis remains one of the deadliest infectious diseases. A plethora of genomic tools and bioinformatics pipelines have become available in recent years to assist the whole genome sequencing of M. tuberculosis. The Oxford Nanopore Technologies (ONT) portable sequencer is a promising platform for cost-effective application in clinics, including personalizing treatment through detection of drug resistance-associated mutations, or in the field, to assist epidemiological and transmission investigations. In this study, we performed a comparison of 10 clinical isolates with DNA sequenced on both long-read ONT and (gold standard) short-read Illumina HiSeq platforms. Our analysis demonstrates the robustness of the ONT variant calling for single nucleotide polymorphisms, despite the high error rate. Moreover, because of improved coverage in repetitive regions where short sequencing reads fail to align accurately, ONT data analysis can incorporate additional regions of the genome usually excluded (e.g. pe/ppe genes). The resulting extra resolution can improve the characterization of transmission clusters and dynamics based on inferring closely related isolates. High concordance in variants in loci associated with drug resistance supports its use for the rapid detection of resistant mutations. Overall, ONT sequencing is a promising tool for TB genomic investigations, particularly to inform clinical and surveillance decision-making to reduce the disease burden.
More accurate estimation of cell composition in bulk expression through robust integration of single-cell information
Authors: Karimnezhad Ali
Published: July 2022

Motivation

The rapid single-cell transcriptomic technology developments have led to an increasing interest in cellular heterogeneity within cell populations. Although cell-type proportions can be obtained directly from single-cell RNA sequencing (scRNA-seq), it is costly and not feasible in every study. Alternatively, with fewer experimental complications, cell-type compositions are characterized from bulk RNA-seq data. Many computational tools have been developed and reported in the literature. However, they fail to appropriately incorporate the covariance structures in both scRNA-seq and bulk RNA-seq datasets in use.

Results

We present a covariance-based single-cell decomposition (CSCD) method that estimates cell-type proportions in bulk data through building a reference expression profile based on a single-cell data, and learning gene-specific bulk expression transformations using a constrained linear inverse model. The approach is similar to Bisque, a cell-type decomposition method that was recently developed. Bisque is limited to a univariate model, thus unable to incorporate gene-gene correlations into the analysis. We introduce a more advanced model that successfully incorporates the covariance structures in both scRNA-seq and bulk RNA-seq datasets into the analysis, and fixes the collinearity issue by utilizing a linear shrinkage estimation of the corresponding covariance matrices. We applied CSCD to several publicly available datasets and measured the performance of CSCD, Bisque and six other common methods in the literature. Our results indicate that CSCD is more accurate and comprehensive than most of the existing methods.

Availability and implementation

The R package is available on https://github.com/empiricalbayes/CSCDRNA.
Island of misfit tortoises: waif gopher tortoise health assessment following translocation
Authors: McKee Rebecca K , Buhlmann Kurt A , Moore Clinton T , Allender Matthew C , Stacy Nicole I , Tuberville Tracey D
Published: July 2022

Translocation, the intentional movement of animals from one location to another, is a common management practice for the gopher tortoise (Gopherus polyphemus). Although the inadvertent spread of pathogens is a concern with any translocation effort, waif tortoises—individuals that have been collected illegally, injured and rehabilitated or have unknown origins—are generally excluded from translocation efforts due to heightened concerns of introducing pathogens and subsequent disease to naïve populations. However, repurposing these long-lived animals for species recovery is desirable when feasible, and introducing waif tortoises may bolster small populations facing extirpation. The objective of this study was to assess the health of waif tortoises experimentally released at an isolated preserve in Aiken County, SC, USA. Our assessments included visual examination, screening for 14 pathogens using conventional or quantitative polymerase chain reaction (qPCR) and haematological evaluation. Of the 143 individuals assessed in 2017 and 2018, most individuals (76%; n = 109 of 143) had no overt clinical evidence of disease and, when observed, clinical findings were mild. In both years, we detected two known tortoise pathogens, Mycoplasma agassizii and Mycoplasma testudineum, at a prevalence of 10.2–13.9% and 0.0–0.8%, respectively. Additionally, we found emydid Mycoplasma, a bacterium commonly found in box turtles (Terrapene spp.), in a single tortoise that showed no clinical evidence of infection. The presence of nasal discharge was an important, but imperfect, predictor of Mycoplasma spp. infection in translocated tortoises. Hemogram data were comparable with wild populations. Our study is the first comprehensive effort to assess pathogen prevalence and hemogram data of waif gopher tortoises following translocation. Although caution is warranted and pathogen screening necessary, waif tortoises may be an important resource for establishing or augmenting isolated populations when potential health risks can be managed.
Aeromonas salmonicida intraspecies divergence revealed by the various strategies displayed when grazed by Tetrahymena pyriformis
Authors: Paquet Valérie E , Durocher Alicia F , Charette Steve J
Published: July 2022

Worldwide, Aeromonas salmonicida is a major bacterial pathogen of fish in both marine and freshwater environments. Despite psychrophilic growth being common for this species, the number of characterized mesophilic strains is increasing. Thus, this species may serve as a model for the study of intraspecies lifestyle diversity. Although bacteria are preyed upon by protozoan predators, their interaction inside or outside the phagocytic pathway of the predator can provide several advantages to the bacteria. To correlate intraspecies diversity with predation outcome, we studied the fate of psychrophilic and mesophilic strains of A. salmonicida cocultured with the ciliate Tetrahymena pyriformis. A total of three types of outcome were observed: digestion, resistance to phagocytosis, and pathogenicity. The psychrophilic strains are fully digested by the ciliate. In contrast, the mesophilic A. salmonicida subsp. pectinolytica strain is pathogenic to the ciliate. All the other mesophilic strains display mechanisms to resist phagocytosis and/or digestion, which allow them to survive ciliate predation. In some cases, passage through the phagocytic pathway resulted in a few mesophilic A. salmonicida being packaged inside fecal pellets. This study sheds light on the great phenotypic diversity observed in the complex range of mechanisms used by A. salmonicida to confront a predator.
Transcriptome analysis of peach fruit under 1-MCP treatment provides insights into regulation network in melting peach softening
Authors: Qian Jianpu , Zhao Yingjie , Shi Yanna , Chen Kunsong
Published: July 2022

Peach (Prunus persica L.) displays distinguish texture phenotype during postharvest, which could be classified into three types, including melting flesh (MF), non-melting flesh, and stony-hard. MF peach would soften rapidly with an outbreak of ethylene production, which causes huge wastage during fruit transportation and storage. 1-Methylcyclopropene (1-MCP) was used to alleviate fruit softening. In this study, we performed RNA-sequencing on two MF peach cultivars (‘YuLu’ and ‘Yanhong’) after 1-MCP treatment to identify the candidate genes participating in peach fruit softening. A total of 167 genes were identified by weighted gene coexpression network analysis and correlation analysis that could respond to 1-MCP treatment and might be related to softening. Among them, 5 auxin-related genes including 2 indole-3-acetic acid, 1 auxin response transcription factor and 2 small auxin-up RNAs, and 4 cell wall modifying genes (PpPG1, PpPG2, PpPG24 and PpPMEI) were characterized as key genes participating in MF peach softening. Furthermore, 2 transcription factors, which belong to HD-ZIP and MYB, were predicted as candidates regulating softening process by constructing a transcriptional network of these 4 cell wall modifying genes combined with expression pattern analysis, of which HD-ZIP could trans-activate the promoter of PpPG1.
Beyond editing, CRISPR/Cas9 for protein localization: an educational primer for use with “A dCas9-based system identifies a central role for Ctf19 in kinetochore-derived suppression of meiotic recombination”
Authors: McVey Shelby L , Olson Mischa A , Pawlowski Wojciech P , Nannas Natalie J
Published: July 2022

CRISPR/Cas9 has dramatically changed how we conduct genetic research, providing a tool for precise sequence editing. However, new applications of CRISPR/Cas9 have emerged that do not involve nuclease activity. In the accompanying article “A dCas9-based system identifies a central role for Ctf19 in kinetochore-derived suppression of meiotic recombination,” Kuhl et al. utilize a catalytically dead Cas9 to localize proteins at specific genomic locations. The authors seek to understand the role of kinetochore proteins in the suppression of meiotic recombination, a phenomenon that has been observed in centromere regions. By harnessing the power of CRISPR/Cas9 to bind specific genomic sequences, Kuhl et al. localized individual kinetochore proteins to areas of high meiotic recombination and assessed their role in suppression. This primer article provides undergraduate students with background information on chromosomes, meiosis, recombination and CRISPR/Cas9 to support their reading of the Kuhl et al. study. This primer is intended to help students and instructors navigate the study’s experimental design, interpret the results, and appreciate the broader scope of meiotic recombination and CRISPR/Cas9. Questions are included to facilitate discussion of the study.
The DNA replication protein Orc1 from the yeast Torulaspora delbrueckii is required for heterochromatin formation but not as a silencer-binding protein
Authors: Maria Haniam , Rusche Laura N
Published: July 2022

To understand the process by which new protein functions emerge, we examined how the yeast heterochromatin protein Sir3 arose through gene duplication from the conserved DNA replication protein Orc1. Orc1 is a subunit of the origin recognition complex (ORC), which marks origins of DNA replication. In Saccharomyces cerevisiae, Orc1 also promotes heterochromatin assembly by recruiting the structural proteins Sir1-4 to silencer DNA. In contrast, the paralog of Orc1, Sir3, is a nucleosome-binding protein that spreads across heterochromatic loci in conjunction with other Sir proteins. We previously found that a nonduplicated Orc1 from the yeast Kluyveromyces lactis behaved like ScSir3 but did not have a silencer-binding function like ScOrc1. Moreover, K. lactis lacks Sir1, the protein that interacts directly with ScOrc1 at the silencer. Here, we examined whether the emergence of Sir1 coincided with Orc1 acting as a silencer-binding protein. In the nonduplicated species Torulaspora delbrueckii, which has an ortholog of Sir1 (TdKos3), we found that TdOrc1 spreads across heterochromatic loci independently of ORC, as ScSir3 and KlOrc1 do. This spreading is dependent on the nucleosome binding BAH domain of Orc1 and on Sir2 and Kos3. However, TdOrc1 does not have a silencer-binding function: T. delbrueckii silencers do not require ORC-binding sites to function, and Orc1 and Kos3 do not appear to interact. Instead, Orc1 and Kos3 both spread across heterochromatic loci with other Sir proteins. Thus, Orc1 and Sir1/Kos3 originally had different roles in heterochromatin formation than they do now in S. cerevisiae.
Endogenous ceramide phosphoethanolamine modulates circadian rhythm via neural–glial coupling in Drosophila
Authors: Chen Xiupeng , Li Jie , Gao Zhongbao , Yang Yang , Kuang Wenqing , Dong Yue , Chua Gek Huey , Huang Xiahe , Jiang Binhua , Tian He , Wang Yingchun , Huang Xun , Li Yan , Lam Sin Man , Shui Guanghou
Published: July 2022

While endogenous lipids are known to exhibit rhythmic oscillations, less is known about how specific lipids modulate circadian behavior. Through a series of loss-of-function and gain-of-function experiments on ceramide phosphoethanolamine (CPE) synthase of Drosophila, we demonstrated that pan-glial-specific deficiency in membrane CPE, the structural analog of mammalian sphingomyelin (SM), leads to arrhythmic locomotor behavior and shortens lifespan, while the reverse is true for increasing CPE. Comparative proteomics uncovered dysregulated synaptic glutamate utilization and transport in CPE-deficient flies. An extensive genetic screen was conducted to verify the role of differentially expressed proteins in circadian regulation. Arrhythmic locomotion under cpes1 mutant background was rescued only by restoring endogenous CPE or SM through expressing their respective synthases. Our results underscore the essential role of CPE in maintaining synaptic glutamate homeostasis and modulating circadian behavior in Drosophila. The findings suggest that region-specific elevations of functional membrane lipids can benefit circadian regulation.
Widespread bird species show idiosyncratic responses in residual body mass to selective logging and edge effects in the Colombian Western Andes
Authors: Jones Harrison H , Colorado Z. Gabriel , Robinson Scott K
Published: July 2022

Forest fragmentation is a major driver of tropical bird endangerment, yet the mechanisms underlying species losses in fragmented landscapes remain poorly known. Loss of foraging microhabitats and food diversity in fragmented landscapes are potential mechanisms explaining fragmentation sensitivity. We, therefore, measured the body condition (i.e., body mass adjusted for individual size) of 20 tropical understory birds as a proxy for food availability across gradients of fragment patch size and silvicultural histories in the Western Andes of Colombia. Specifically, we asked (1) if body condition correlates with patch size, edge effects, or selective logging disturbance; and (2) if species responses were driven by the same explanatory variables or varied idiosyncratically. We documented significant variation in body condition with covariates in 11 of 20 (55%) understory bird species, and 55% of significant correlations were with fragmentation and selective-logging associated variables. Species responses were idiosyncratic and contrasting, with at least 1 significant response to each fragmentation-related covariate. Most effects, however, were driven by logging-induced changes to vegetation structure including loss of large-diameter trees, reduction in foliage height diversity and canopy cover, and loss of understory vegetation. The body condition of frugivores and nectarivores increased with logging-induced shifts in vegetation structure, with canopy gaps potentially favoring early-successional fruiting and flowering plants. By contrast, some insectivores suffered lower body condition with loss of vegetation structure (reduced foliage height diversity). Overall, our data support the hypothesis that fragmentation and selective logging change food resources available to birds and that some widespread nectarivores, frugivores, and omnivores may benefit from increasing edge density and logging-driven vegetation disturbance. We also documented significant positive effects of breeding condition on body condition, however, highlighting the need to control for this factor. Body condition may therefore be a useful index of habitat suitability when paired with analyses of abundance and demographic changes.
A hnRNPA2B1 agonist effectively inhibits HBV and SARS-CoV-2 omicronin vivo
Authors: Zuo Daming , Chen Yu , Cai Jian-piao , Yuan Hao-Yang , Wu Jun-Qi , Yin Yue , Xie Jing-Wen , Lin Jing-Min , Luo Jia , Feng Yang , Ge Long-Jiao , Zhou Jia , Quinn Ronald J , Zhao San-Jun , Tong Xing , Jin Dong-Yan , Yuan Shuofeng , Dai Shao-Xing , Xu Min
Published: July 2022

The twenty-first century has already recorded more than ten major epidemics or pandemics of viral disease, including the devastating COVID-19. Novel effective antivirals with broad-spectrum coverage are urgently needed. Herein, we reported a novel broad-spectrum antiviral compound PAC5. Oral administration of PAC5 eliminated HBV cccDNA and reduced the large antigen load in distinct mouse models of HBV infection. Strikingly, oral administration of PAC5 in a hamster model of SARS-CoV-2 omicron (BA.1) infection significantly decreases viral loads and attenuates lung inflammation. Mechanistically, PAC5 binds to a pocket near Asp49 in the RNA recognition motif of hnRNPA2B1. PAC5-bound hnRNPA2B1 is extensively activated and translocated to the cytoplasm where it initiates the TBK1-IRF3 pathway, leading to the production of type I IFNs with antiviral activity. Our results indicate that PAC5 is a novel small-molecule agonist of hnRNPA2B1, which may have a role in dealing with emerging infectious diseases now and in the future.
Real-world use of an etanercept biosimilar including selectiveversusautomatic substitution in inflammatory arthritis patients: a UK-based electronic health records study
Authors: Cooksey Roxanne , Brophy Sinead , Kennedy Jonathan , Seaborne Michael , Choy Ernest
Published: July 2022

Objective

Biosimilars are approved as an alternative treatment to their originators. We compared the clinical outcomes of etanercept (ETN) biosimilar compared with ETN originator in real-world practice, from two local health boards in Wales with different policies on switching: automatic vs selective.

Methods

Data from the Secure Anonymised Information Linkage (SAIL) databank in Wales were used to create a retrospective cohort study using linked primary and secondary care data. Patients aged ≥18 years with diagnosis codes for RA, PsA or AS were included. Outcomes included treatment failure and DAS-28 score (for RA). The local health board with a policy of automatic switching (i.e. clinician/nurse involvement not mandated) is labelled as automatic switch area, and the other, which required clinician/nurse supervision, as selective switch.

Results

Of 8925 individuals with inflammatory arthritis, 13.3% (365) received ETN biosimilar and 31.5% (863) ETN originator. The treatment discontinuation rate was similar for ETN biosimilar and originator by Kaplan–Meier analysis. More biosimilar failure patients were treated in the automatic switch area (15 vs 4.8%). In the automatic switch area, 28.8% (75 of 260) of patients switched automatically from ETN originator to biosimilar compared with 10.5% (11 of 105) in the selective switch area. ETN biosimilar reduced DAS-28 by 1.6 ± 1.8 in the selective switch area vs 0.4 ± 0.6 in the automatic switch area.

Conclusion

The ETN biosimilar was well tolerated. Fewer people were switched using selective policy, but this was associated with lower failure rates. Automatic switch policy led to more patients being switched and did not lead to significant worsening of disease.
John Dryden’s Sister Arts: Face-Painting and Translation
Authors: Zou Qifei
Published: July 2022

This essay explores an alternative figuration in Dryden’s thought and writing on the sister arts: face-painting and translation. In this parallel, Dryden conceives of the face as the original text, the face-paint as the translated word, the cosmetician as the translator, and vice versa. To explore the interrelationship of these arts is to reveal the contradictory impulses that shape Dryden’s 1697 Aeneis, reconciling opposing critical views of his translation strategies. In this essay, I survey the prevalent satiric and aesthetic functions of face-painting in Dryden’s writings. I show that in his essays of the 1690s, Dryden’s ambivalent views on cosmetics inform his views on translation: both the original text and the unpainted face are sacred designs that, paradoxically, may still be beautified by the translator’s expression or the cosmetician’s paint. In translation, Dryden is thus caught between the desire to foreground his own paint and the obligation to preserve Virgil’s design. By way of conclusion, I offer a reading of Dryden’s three renderings of the Aeneas and Lausus episode (Aeneid X), in which he liberally daubs and delicately paints upon Virgil’s original. These diverse strategies are poetic manifestations of the conflicting energies that define Dryden’s sister arts, face-painting and translation.
Refugee Women and the Gendered Violence of Australia’s Extraterritorial Asylum Regime on Nauru
Authors: Vasefi Saba , Dehm Sara
Published: July 2022

This article examines the gendered harms of state refugee externalisation laws and policies using the case study of Australia’s extraterritorial asylum regime on Nauru. While the regime has been widely criticised, the particular carceral experiences and structural vulnerabilities of refugee women and girls have received limited attention in refugee law scholarship. Drawing on interviews with 10 refugee women, this article documents and conceptualises the abusive nature of the regime from a gender perspective: first in relation to the produced insecurity and sexual violence in immigration detention and temporary resettlement in Nauru; next, in relation to the gendered medicalisation of refugee bodies under the official medical evacuation processes for transferring refugees from Nauru to Australia for healthcare; and finally, in relation to the continued punitive legal limbo and produced deportability for refugee women once transferred to Australia who nonetheless remain subject to the legal exclusions under Australia’s “offshore” detention and processing regime. We argue that, rather than being incidental to its operation, gendered harms have become a defining feature of the structural violence of Australia’s deterrence framework and practices of refugee expulsion and exclusion.
Bunk space requirements for growing beef cattle limit-fed a high-energy corn and corn co-product diet
Authors: Duncan Zachary M , DeBord Zachary L , Pflughoeft Madison G , Suhr Kyler J , Hollenbeck William R , Tarpoff Anthony J , Olson K C , Blasi Dale A
Published: July 2022

Bunk requirements for optimal growth performance of growing calves limit-fed high-energy corn and corn co-product diets have not been widely evaluated. Three-hundred eighty-five crossbred steers (initial body weight = 215 ± 25 kg) were purchased in Texas, transported to the Kansas State Beef Stocker Unit, and weighed at arrival. Steers were stratified by body weight and randomly assigned to 1 of 28 pens containing 12 to 14 head. Within block, pens were randomly assigned to one of four bunk allotment treatments: 25.4, 38.1, 50.8, or 63.5 cm of bunk per head for a 58-d receiving period. Calves were fed at 0700 h once daily at 1.8% of bodyweight (dry matter basis) from February 2 to March 13, 2021; thereafter the daily feed allotment was increased to 2.0% of bodyweight. The diet contained (dry matter basis) 39.5% dry-rolled corn, 7.5% supplement, 40% wet corn gluten feed, and 13% prairie hay. Steers were individually weighed on days 29 and 58 and pen weights were measured weekly to determine feed offered for the following week. Body weights on days 29 and 58, dry matter intake, or gain-to-feed ratio during the receiving period did not differ (P ≥ 0.34) between treatments. During the first 29 d, average daily gain (ADG) increased linearly as bunk space increased (P = 0.03); however, no treatment effects were observed thereafter. In addition, ADG standard deviation from days 0 to 29 responded quadratically (P = 0.05) where ADG standard deviation tended to be greater in the 38.1-cm allotment and was greater in the 50.8-cm allotment compared to the 25.4-cm allotment (P = 0.07 and P = 0.04, respectively). Bunk score tended to decrease linearly as bunk allotment decreased (P = 0.06). Following the receiving period, steers were blocked by bunk treatment and randomly assigned to 1 of 18 pastures. Steers were grazed for 90-d from May to August at a targeted stocking density of 280 kg live-weight ˖ ha–1. During the grazing season, ADG increased linearly with reduced (P < 0.01) bunk allotment; however, body weights did not differ (P = 0.91) between bunk treatments at the completion of the grazing period. In addition, overall total body weight gains and ADG from the receiving and grazing periods did not differ (P > 0.57) between bunk treatments. We interpreted our data to suggest that bunk space allotments of 25.4 to 63.5 cm per head had minimal impact on growth performance during a 58-d receiving period and did not affect final body weights following a 90-d grazing season.
New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria
Authors: Zucker Falk , Bischoff Vera , Olo Ndela Eric , Heyerhoff Benedikt , Poehlein Anja , Freese Heike M , Roux Simon , Simon Meinhard , Enault Francois , Moraru Cristina
Published: July 2022

The Microviridae family represents one of the major clades of single-stranded DNA (ssDNA) phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in the genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteriaceae and cluster within the ‘Alpavirinae’, ‘Amoyvirinae’, and Gokushovirinae. We have isolated ‘Ascunsovirus oldenburgi’ ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources sixty-five new Microviridae prophages and episomes in bacterial genomes and retrieved forty-seven environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named ‘Tainavirinae’ and ‘Occultatumvirinae’. They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here sheds light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.
Summating Potential as Marker of Intracochlear Position in Bipolar Electrocochleography
Authors: Baumhoff Peter , Rahbar Nikoukar Laya , de Andrade José Santos Cruz , Lenarz Thomas , Kral Andrej
Published: July 2022

Objectives:

Cochlear implantation criteria include subjects with residual low-frequency hearing. To minimize implantation trauma and to avoid unwanted interactions of electric- and acoustic stimuli, it is often recommended to stop cochlear implantation before the cochlear implant (CI) reaches the cochlear partition with residual hearing, as determined by an audiogram. For this purpose, the implant can be used to record acoustically evoked signals during implantation, including cochlear compound action potentials (CAP), cochlear microphonics (CMs), and summating potentials (SPs). The former two have previously been used to monitor residual hearing in clinical settings.

Design:

In the present study we investigated the use of intracochlear, bipolar SP recordings to determine the exact cochlear position of the contacts of implanted CIs in guinea pig cochleae (n = 13). Polarity reversals of SPs were used as a functional marker of intracochlear position. Micro computed tomography (µCT) imaging and a modified Greenwood function were used to determine the cochleotopic positions of the contacts in the cochlea. These anatomical reconstructions were used to validate the SP-based position estimates.

Results:

The precision of the SP-based position estimation was on average within ± 0.37 octaves and was not impaired by moderate hearing loss caused by noise exposure after implantation. It is important to note that acute hearing impairment did not reduce the precision of the method. The cochleotopic position of CI accounted for ~70% of the variability of SP polarity reversals. Outliers in the dataset were associated with lateral CI positions. Last, we propose a simplified method to avoid implantation in functioning parts of the cochlea by approaching a predefined frequency region using bipolar SP recordings through a CI.

Conclusions:

Bipolar SP recordings provide reliable information on electrode position in the cochlea. The position estimate remains reliable after moderate hearing loss. The technique presented here could be applied during CI surgery to monitor the CI approach to a predefined frequency region.
Innovations in Breastfeeding Support
Authors: Mestre Cathleen T. , Excellent Darchelle , Jaynes Shewit , Louis-Jacques Adetola F.
Published: July 2022

Despite the numerous benefits that breastfeeding confers to those who breastfeed and their infants, the United States’ exclusive breastfeeding rates and any breastfeeding rates at 12 months remain low and inequitable. This public health crisis has been prioritized in the US Healthy People 2030 goals. Current evidence-based practices to support lactation have afforded limited progress, thus, achieving national breastfeeding goals requires innovative ideas in thinking, technology, and care. This article highlights potential innovative strategies in the field of lactation to improve outcomes and work toward achieving health equity, while underscoring the critical role that perinatal caregivers play in lactation support.
Exploring the Link Between the Serum/Blood Levels of Heavy Metals (Pb, As, Cd, and Cu) and 2 Novel Biomarkers of Cardiovascular Stress (Growth Differentiation Factor 15 and Soluble Suppression of Tumorigenicity 2) in Copper Smelter Workers
Authors: Mourad Basma Hussein , El-Sherif Ghada Hossam
Published: July 2022

Objective

Studying the association between the occupational exposure to Pb, As, Cd, and Cu with the serum levels of 2 novel biomarkers of cardiovascular stress; growth differentiation factor 15 and soluble suppression of tumorigenicity 2, in some Egyptian Cu smelter workers.

Methods

Forty-one exposed workers and 41 administrative controls were clinically evaluated. Serum/blood levels of heavy metals and biomarkers were measured for both groups.

Results

The smelter workers showed significantly elevated levels of heavy metals and biomarkers compared with controls. The elevated serum levels of both biomarkers were significantly and positively correlated with each other, the levels of heavy metals, and the duration of employment of the exposed workers.

Conclusions

There was a significant association between the levels of heavy metals and both biomarkers among the smelter workers. Further prospective studies should be performed.
A Review of Treatments and Clinical Guidelines for Perinatal Depression
Authors: McDonald Maria , Alhusen Jeanne
Published: July 2022

Perinatal depression occurs in approximately 1 in 7 women and is considered the most common complication of pregnancy and childbearing. Management of perinatal depression may include a combination of nonpharmacological and pharmacological therapies depending on the severity of symptoms, the stage of gestation, and maternal preference. Healthcare providers are recommended to review current guidelines and provide information to women during pregnancy and postpartum regarding the risks and benefits of nonpharmacological and pharmacological treatment options for perinatal depression. In addition, healthcare providers should consider common barriers to treatment including inadequate screening and social stigma. This article reviews common treatments of perinatal depression as well as the clinical guidelines provided by the American Association of Obstetricians and Gynecologists (ACOG), the American Psychiatric Association (APA), and the US Preventive Services Task Force (USPSTF). Discussion of nonpharmacological therapies includes cognitive behavioral therapy (CBT) and interpersonal therapy (IPT). Pharmacological treatments are reviewed by drug class and include selective serotonin reuptake inhibitors (SSRIs), serotonin/norepinephrine reuptake inhibitors (SNRIs), norepinephrine/dopamine reuptake inhibitors (NDRIs), and tricyclic antidepressants (TCAs). Adjunctive treatments of severe depression, including second-generation antipsychotics (SGAs), are also discussed.
Aerosol Generation During Otologic Surgery
Authors: Lahelma Mari , Oksanen Lotta , Rantanen Noora , Sinkkonen Saku , Aarnisalo Antti , Geneid Ahmed , Sanmark Enni
Published: July 2022

Objective

To assess whether aerosol generation occurs during otologic surgery, to define which instruments are aerosol generating, and to identify factors that enhance safety in protection against airborne pathogens, such as severe acute respiratory syndrome coronavirus 2.

Study Design

An observational prospective study on aerosol measurements during otologic operations recorded between August and December 2020.

Setting

Aerosol generation was measured with an Optical Particle Sizer as part of otologic operations with anesthesia. Particles with a size range of 0.3 to 10 μm were quantified. Aerosol generation was measured during otologic operations to analyze aerosols during drilling in transcanal and transmastoid operations and when using the following instruments: bipolar electrocautery, laser, suction, and cold instruments. Coughing is known to produce significant concentration of aerosols and is commonly used as a reference for high-risk aerosol generation. Thus, the operating room background concentration and coughing were chosen as reference values.

Patients

Thirteen otologic operations were included. The average drilling time per surgery was 27.00 minutes (range, 2.00–71.80 min).

Intervention

Different rotation speeds during drilling and other instruments were used.

Main Outcome Measures

Aerosol concentrations during operations were recorded and compared with background and cough aerosol concentrations.

Results

Total aerosol concentrations during drilling were significantly higher than background (p < 0.0001, d = 2.02) or coughing (p < 0.0001, d = 0.50). A higher drilling rotation speed was associated with higher particle concentration (p = 0.037, η
2 = 0.01). Aerosol generation during bipolar electrocautery, drilling, and laser was significantly higher than with cold instruments or suction (p < 0.0001, η
2 = 0.04).

Conclusion

High aerosol generation is observed during otologic surgery when drill, laser, or bipolar electrocautery is used. Aerosol generation can be reduced by using cold instruments instead of electric and keeping the suction on during aerosol-generating procedures. If drilling is required, lower rotation speeds are recommended. These measures may help reduce the spread of airborne pathogens during otologic surgery.
Hearing Health Perceptions and Literacy Among Primary Healthcare Providers in the United States: A National Cross-Sectional Survey
Authors: Sydlowski Sarah A. , Marinelli John P. , Lohse Christine M. , Carlson Matthew L. ,   Hearing Health Collaborative
Published: July 2022

Objective

To characterize current awareness, perceptions, and literacy surrounding hearing loss among United States primary healthcare professionals.

Study design

National cross-sectional survey study.

Setting

United States.

Participants

Four hundred six healthcare professionals.

Results

Survey respondents included 205 primary care physicians and 201 nurse practitioners or physician assistants. When compared with 10 other common health conditions, only 1% of respondents ranked hearing loss as a “most important” health condition to manage. Less than half of providers reported recommending hearing testing for their patients at least once per year, whereas evaluation of blood pressure, total cholesterol, body mass index, and blood glucose levels are recommended at least annually by more than 80% of providers. Although 95% of respondents indicated that it is somewhat important or very important for patients to know the standard definition for normal hearing, only 57% of surveyed providers know of a standard definition themselves, and only 28% reported familiarity with the concept of “20/20 hearing.” Conversely, more than 80% of respondents know the “normal” metric for blood pressure, total cholesterol, body mass index, blood glucose, and vision. Most respondents realize that hearing is important to overall health and hearing loss can impact personal safety, lead to social isolation, and negatively impact quality of life. Fifty-four percent also acknowledged a link between hearing loss and depression, but a majority were not very aware of the relationship of hearing loss to risk of falling and dementia, reduced income and job opportunities, and type 2 diabetes. Importantly, only 40% of providers believe hearing loss is treatable, and only 17% believe it is preventable.

Conclusion

Despite widespread literacy of what constitutes normal blood pressure, total cholesterol, body mass index, blood glucose, and vision metrics, healthcare providers exhibit a poor understanding of normal hearing levels. Few providers prioritize hearing health or regularly recommend for annual hearing evaluation. Most providers believe that options for people with hearing loss are limited, which may have important implications for prioritizing discussion of hearing loss with patients.
Assessing Outcomes After Adrenalectomy for Primary Aldosteronism – Early is Accurate
Authors: Suurd Diederik P.D. , Vorselaars Wessel M.C.M. , Van Beek Dirk-Jan , Borel Rinkes Inne H.M. , Spiering Wilko , Valk Gerlof D. , Vriens Menno R.
Published: July 2022

Objective:

We aimed to investigate the postoperative trend in blood pressure (BP)-related outcomes [BP and antihypertensive (AHT) drug use] during the year following adrenalectomy for primary aldosteronism (PA) to determine the optimal timing for outcome assessment and to determine the necessary follow-up length.

Background:

Since the course of BP-related outcomes after adrenalectomy is unknown, the optimal timing of outcome assessment and follow-up duration are not clear.

Methods:

In this retrospective single center cohort study, we used a prospectively collected database with all patients referred for difficult-to-control-hypertension-analysis. All patients diagnosed with PA who underwent adrenalectomy were included. AHT drug use [in defined daily dose (DDD)] and home blood pressure measurements (HBPMs) during the first postoperative year were collected. A mixed-effects model was developed to assess the stability of DDD and HBPM over time and adjust for potential confounders.

Results:

In total 1784 patients were assessed for difficult-to-control-hypertension of whom 41 were included. Both the DDD and HBPM showed the strongest decrease in the first postoperative month (mean 1.6DDD; mean 140/85 mm Hg) compared with preoperative values (4.5DDD; 153/92 mm Hg). Thereafter, both outcomes showed a stable course from 4 to 6 months (1.6DDD; 136/86 mm Hg) up to 12 months postoperatively (2.0DDD; 136/83 mm Hg).

Conclusions:

This study showed that AHT drug use and HBPM decreased substantially within the first month after adrenalectomy for PA and afterwards generally remained stable during the year following adrenalectomy. We propose that BP-related outcomes can be assessed reliably early after adrenalectomy and question the need for routine long-term follow-up in referral centers.
Andrew Clennel Palmer. 26 May 1938—21 December 2019
Authors: King Roger Antony
Published: July 2022

Andrew Clennel Palmer was internationally recognized for his major works on submarine pipeline design and engineering, although his work on the properties of ice and arctic engineering is equally noteworthy. His early research work at Cambridge, Brown and Liverpool Universities related to the mechanical properties of soils and sediments and the effect of temperature; this led to him aiding with the design of the trans-Alaska pipeline and work on major oil and gas pipelines in the UK sector of the North Sea. Andrew's successes drew him deeper into pipeline engineering and he worked with R. J. Brown & Associates in Houston, Texas, and in Holland, becoming vice-president and head of the London office in 1982. During a lull in the pipeline industry, Andrew returned to academe at the University of Manchester Institute of Science and Technology to develop a new course in offshore engineering. When the pipeline engineering industry recovered, Andrew started a company specializing in solving the many complex problems resulting from the installation of pipelines in ever-deeper waters. Andrew returned to Cambridge in 1996 as the first Research Professor of Petroleum Engineering in the Department of Engineering, a new post supported by the Jafar Foundation. He led a vigorous research group with strong connections to the pipeline industry, becoming president of the Pipeline Industries Guild in 1998; and he returned to the study of ice forces on offshore structures, also working with the university's Scott Polar Research Institute. On his retirement from Cambridge, Andrew moved to the National University of Singapore in 2006 as Keppel Chair Professor in the Department of Civil Engineering.
The quantum theory of time: a calculus for q-numbers
Authors: Kuypers Samuel
Published: July 2022

In quantum theory, physical systems are usually assumed to evolve relative to a c-number time. This c-number time is unphysical and has turned out to be unnecessary for explaining dynamics: in the timeless approach to quantum theory developed by Page & Wootters 1983
Phys. Rev. D
27
, 2885. (
doi:10.1103/PhysRevD.27.2885
), subsystems of a stationary universe can instead evolve relative to a ‘clock', which is a quantum system with a q-number time observable. Page & Wootters formulated their construction in the Schrödinger picture, which left open the possibility that the c-number time still plays an explanatory role in the Heisenberg picture. I formulate their construction in the Heisenberg picture and demonstrate how to eliminate c-number time from that picture, too. When the Page–Wootters construction is formulated in the Heisenberg picture, the descriptors of physical systems are functions of the clock's q-number time, and derivatives with respect to this q-number time can be defined in terms of the clock's algebra of observables, which results in a calculus for q-numbers.
Integrable nonlinear evolution equations in three spatial dimensions
Authors: Fokas A. S.
Published: July 2022

There are integrable nonlinear evolution equations in two spatial variables. The solution of the initial value problem of these equations necessitated the introduction of novel mathematical formalisms. Indeed, the classical Riemann–Hilbert problem used for the solution of integrable equations in one spatial variable was replaced by a non-local Riemann–Hilbert problem or, more importantly, by the so-calledd-bar formalism. The construction of integrable nonlinear evolution equations in three spatial dimensions has remained the key open problem in the area of integrability. For example, the two versions of the Kadomtsev–Petviashvili (KP) equation constitute two-dimensional generalizations of the celebrated Korteweg–de Vries equation. Are there three-dimensional generalizations of the KP equations? Here, we present such equations. Furthermore, we introduce a novel non-locald-bar formalism for solving the associated initial value problem.
Does functional redundancy determine the ecological severity of a mass extinction event?
Authors: Dick Daniel G. , Darroch Simon , Novack-Gottshall Philip , Laflamme Marc
Published: July 2022

Many authors have noted the apparent ‘decoupling’ of the taxonomic and ecological severity of mass extinction events, with no widely accepted mechanistic explanation for this pattern having been offered. Here, we test between two key factors that potentially influence ecological severity: biosphere entropy (a measure of functional redundancy), and the degree of functional selectivity (in terms of deviation from a pattern of random extinction with respect to functional entities). While theoretical simulations suggest that the Shannon entropy of a given community prior to an extinction event determines the expected outcome following a perturbation of a given magnitude, actual variation in Shannon entropy between major extinction intervals is insufficient to explain the observed variation in ecological severity. Within this information-theoretic framework, we show that it is the degree of functional selectivity that is expected to primarily determine the ecological impact of a given perturbation when levels of functional redundancy are not substantially different.