bluuebunny/crossref_metadata_2025 huggingface dataset:
Human stem cell model ofHNF1Adeficiency shows uncoupled insulin to C-peptide secretion with accumulation of abnormal insulin granules
Authors: González Bryan J. , Zhao Haoquan , Niu Jacqueline , Williams Damian J. , Lee Jaeyop , Goulbourne Chris N. , Xing Yuan , Wang Yong , Oberholzer Jose , Chen Xiaojuan , LeDuc Charles A. , Chung Wendy K. , Colecraft Henry M. , Gromada Jesper , Shen Yufeng , Goland Robin S. , Leibel Rudolph L. , Egli Dieter
Published: January 2021

Mutations inHNF1Acause Maturity Onset Diabetes of the Young type 3 (MODY3), the most prevalent form of monogenic diabetes. We generated stem cell-derived pancreatic endocrine cells from human embryonic stem cells (hESCs) with induced hypomorphic mutations inHNF1A. Using these cells, we show thatHNF1Aorchestrates a transcriptional program required for distinct aspects of β-cell fate and function. During islet cell differentiation,HNF1Adeficiency biases islet endocrine cells towards anα-cell fate associated withPAX4down-regulation.HNF1A-deficient β-cells display impaired basal and glucose stimulated-insulin secretion in association with a reduction inCACNA1Aand intracellular calcium levels, and impaired insulin granule exocytosis in association withSYT13down-regulation. Knockout ofPAX4,CACNA1AandSYT13reproduce the relevant phenotypes. Reduction of insulin secretion is associated with accumulation of enlarged secretory granules, and altered stoichiometry of secreted insulin to C-peptide. InHNF1Adeficient β-cells, glibenclamide, a sulfonylurea drug used in the treatment of MODY3 patients, increases intracellular calcium to levels beyond those achieved by glucose, and restores C-peptide and insulin secretion to a normal stoichiometric ratio. To studyHNF1Adeficiency in the context of a human disease model, we also generated stem cell-derived pancreatic endocrine cells from two MODY3 patient’s induced pluripotent stem cells (iPSCs). While insulin secretion defects are constitutive in cells with completeHNF1Aloss of function, β-cells heterozygous for hypomorphicHNF1Amutations are initially normal, but lose the ability to secrete insulin and acquire abnormal stoichiometric secretion ratios. Importantly, the defects observed in these stem cell models are also seen in circulating proportions of insulin:C-peptide in nine MODY3 patients.

One sentence of summary

Deficiency of the transcription factorHNF1Abiases islet endocrine cell fate towardsα-cells, impairs intracellular calcium homeostasis and insulin exocytosis, alters the stoichiometry of insulin to C-peptide release, and leads to an accumulation of abnormal insulin secretory granules in β-cells.
Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex
Authors: Leigh D.M. , Lischer H.E.L. , Guillaume F. , Grossen C. , Günther T.
Published: January 2021

Identifying local adaptation in bottlenecked species is essential for effective conservation management. Selection detection methods are often applied to bottlenecked species and have an important role in species management plans, assessments of the species’ adaptive capacity, and looking for responses to major threats like climate change. Yet, the allele frequency changes driven by selection and exploited in selection detection methods, are similar to those caused by the strong neutral genetic drift expected during a bottleneck. Consequently, it is often unclear what accuracy selection detection methods may offer within bottlenecked populations. In this study, we used simulations to explore if signals of selection could be confidently distinguished from genetic drift across 23 bottlenecked and reintroduced populations of Alpine ibex (Capra ibex). We used the meticulously recorded demographic history of the Alpine ibex to generate a comprehensive simulated SNP data. The simulated SNPs were then used to benchmark the confidence we could place in putative outliers identified through selection scans on empirical Alpine ibex SNP data. Within the simulated dataset, the false positive rates were high for all selection detection methods but fell substantially when two or more selection detection methods were combined. However, the true positive rates were consistently low and became essentially negligible after this increased stringency. Despite the detection of many putative outlier loci in the empirical Alpine ibex RADseq data, none met the threshold needed to distinguish them from genetic drift-driven false positives. Unfortunately, the low true positive rate also creates a paradox, by preventing the exclusion of recent local adaptation within the Alpine ibex.
Fibroblast State Reversal By MBNL1-Dependent Transcriptome Modification Regulates Cardiac Repair
Authors: Bugg Darrian , Bretherton Ross , Beach Kylie , Reese Anna , Gunaje Jagadambika , Flint Galina , DeForest Cole A. , Stempien-Otero April , Davis Jennifer
Published: January 2021

Dynamic fibroblast state transitions are responsible for the heart’s fibrotic response to injury, raising the possibility that tactical control of these transitions could alter maladaptive fibrotic outcomes. Transcriptome maturation by the RNA binding protein Muscleblind Like 1 (MBNL1) has emerged as a potential driver of differentiated cell states. Here genetic lineage tracing of myofibroblasts in the injured heart demonstrated that gains in MBNL1 function corresponded to profibrotic fibroblast states. Similarly, in mice cardiac fibroblast specific MBNL1 overexpression induced a transcriptional myofibroblast profile in healthy cardiac fibroblasts that prevented the fibroproliferative phase of cardiac wound healing. By contrast loss of MBNL1 reverted cardiac fibroblasts to a pro-proliferative epicardial progenitor state that limited cardiac fibrosis following myocardial infarction. This progenitor state transition was associated with an MBNL1-dependent destabilization of the mesenchymal transition gene,Sox9.These findings suggest that MBNL1 regulation of the fibroblast transcriptome drives state transitions underlying cardiac fibrosis and repair.
High-order areas and auditory cortex both represent the high-level event structure of music
Authors: Williams Jamal A. , Margulis Elizabeth H. , Nastase Samuel A. , Chen Janice , Hasson Uri , Norman Kenneth A. , Baldassano Christopher
Published: January 2021

Recent fMRI studies of event segmentation have found that default mode regions represent high-level event structure during movie watching. In these regions, neural patterns are relatively stable during events and shift at event boundaries. Music, like narratives, contains hierarchical event structure (e.g., sections are composed of phrases). Here, we tested the hypothesis that brain activity patterns in default mode regions reflect the high-level event structure of music. We used fMRI to record brain activity from 25 participants (male and female) as they listened to a continuous playlist of 16 musical excerpts, and additionally collected annotations for these excerpts by asking a separate group of participants to mark when meaningful changes occurred in each one. We then identified temporal boundaries between stable patterns of brain activity using a hidden Markov model and compared the location of the model boundaries to the location of the human annotations. We identified multiple brain regions with significant matches to the observer-identified boundaries, including auditory cortex, medial prefrontal cortex, parietal cortex, and angular gyrus. From these results, we conclude that both higher-order and sensory areas contain information relating to the high-level event structure of music. Moreover, the higher-order areas in this study overlap with areas found in previous studies of event perception in movies and audio narratives, including regions in the default mode network.

Significance Statement

Listening to music requires the brain to track dynamics at multiple hierarchical timescales. In our study, we had fMRI participants listen to real-world music (classical and jazz pieces) and then used an unsupervised learning algorithm (a hidden Markov model) to model the high-level event structure of music within participants’ brain data. This approach revealed that default mode brain regions involved in representing the high-level event structure of narratives are also involved in representing the high-level event structure of music. These findings provide converging support for the hypothesis that these regions play a domain-general role in processing events occurring over long timescales.
Identification and Classification of Reverse Transcriptases in Bacterial Genomes and Metagenomes
Authors: Sharifi Fatemeh , Ye Yuzhen
Published: January 2021

Reverse Transcriptases (RTs) are found in different systems including group II introns, Diversity Generating Retroelements (DGRs), retrons, CRISPR-Cas systems, and Abortive Infection (Abi) systems in prokaryotes. Different classes of RTs can play different roles, such as template switching and mobility in group II introns, spacer acquisition in CRISPR-Cas systems, mutagenic retrohoming in DGRs, programmed cell suicide in Abi systems, and recently discovered phage defense in retrons. While some classes of RTs have been studied extensively, others remain to be characterized. There is a lack of computational tools for identifying and characterizing various classes of RTs. In this study, we built a tool (called myRT) for identification and classification of prokaryotic RTs. In addition, our tool provides information about the genomic neighborhood of each RT, providing potential functional clues. We applied our tool to predict and classify RTs in all complete and draft bacterial genomes, and created a collection that can be used for exploration of putative RTs. Application of myRT to gut metagenomes showed that gut metagenomes encode proportionally more RTs related to DGRs, outnumbering retron-related RTs, as compared to the collection of reference genomes. MyRT is both available as a standalone software and also through a website.
40 minutes RT-qPCR Assay for Screening Spike N501Y and HV69-70del Mutations
Authors: Korukluoglu Gulay , Kolukirik Mustafa , Bayrakdar Fatma , Ozgumus Gozde Girgin , Altas Ayse Basak , Cosgun Yasemin , Ketre Kolukirik Canan Zohre
Published: January 2021

A one-step reverse transcription and real-time PCR (RT-qPCR) test was developed for rapid screening (40 minutes) of the Spike N501Y and HV69-70del mutations in SARS-CoV-2 positive samples. The test also targets a conserved region of SARS-CoV-2 Orf1ab as an internal control. The samples containing both the N501Y and HV69-70del mutations are concluded as VOC-202012/01 positive. Samples suspected to be positive for B.1.351 or P.1 are the N501Y positive and HV69-70del negative cases. Limit of detection (LOD) of the kit for Orf1ab target is 500 copies/mL, while that of the N501, Y501 and HV69-70del targets are 5000 copies/mL. The developed assay was applied to 165 clinical samples containing SARS-CoV-2 from 32 different lineages. The SARS-CoV-2 lineages were determined via the next-generation sequencing (NGS). The RT-qPCR results were in 100% agreement with the NGS results that 19 samples were N501Y and HV69-70del positive, 10 samples were N501Y positive and HV69-70del negative, 1 sample was N501Y negative and HV69-70del positive, and 135 samples were N501Y and HV69-70del negative. All the VOC-202012/01 positive samples were detected in people who have traveled from England to Turkey. The RT-qPCR test and the Sanger sequencing was further applied to 1000 SARS-CoV-2 positive clinical samples collected in Jan2021 from the 81 different provinces of Turkey. The RT-qPCR results were in 100% agreement with the Sanger sequencing results that 32 samples were N501Y positive and HV69-70del negative, 4 samples were N501Y negative and HV69-70del positive, 964 samples were N501Y and HV69-70del negative. The specificity of the 40 minutes RT-qPCR assay relative to the sequencing-based technologies is 100%. The developed assay is an advantageous tool for timely and representative estimation of the N501Y positive variants’ prevalence because it allows testing a much higher portion of the SARS-CoV-2 positives in much lower time compared to the sequencing-based technologies.
Application of the SMALP technology to the isolation of GPCRs from low-yielding cell lines
Authors: Tedesco Daniele , Maj Maciej , Malarczyk Paulina , Cingolani Andrea , Zaffagnini Mirko , Wnorowski Artur , Benelli Tiziana , Mazzoni Rita , Bartolini Manuela , Jóźwiak Krzysztof
Published: January 2021

The ability of styrene–maleic acid (SMAc) co-polymers to spontaneously insert into biological membranes can be exploited to extract G protein-coupled receptors (GPCRs) embedded in styrene–maleic acid lipid particles (SMALPs), preserving the native environment around the protein and thus enhancing the feasibility of functional studies. So far, the SMALP technology has been primarily employed on non-mammalian cells and protocols are not optimized for adherent human cell lines, which cannot be harvested in large amounts. In this work, a fine investigation of key parameters affecting the formation of SMALPs was undertaken with the purpose of maximizing the yield of extraction of a recombinant form of human β2-adrenergic receptor (rhβ2AR) from HEK293T cells. The study highlighted an important influence of ionic strength on the membrane solubilization efficiency and GPCR purification yield of SMAc co-polymers: by lowering the salt concentration of all buffers used in previously published SMALP protocols, the water solubility and extraction efficiency of the selected SMAc co-polymer (commercially supplied as a potassium salt) were enhanced. In-line combination of size-exclusion chromatography (SEC) with immobilized metal affinity chromatography (IMAC) allowed further improvement of the final rhβ2AR yield by reducing the loss of SMALP-embedded GPCRs during the fractionation and purification of SMALPs. The overall findings of this study show that the available SMALP protocols can be significantly optimized in several aspects in order to increase the efficiency of GPCR solubilization and isolation from low-yielding expression systems.

Highlights

The SMALP technology enables a direct solubilization of GPCRs from cell membranes.

The isolation of GPCRs from mammalian cells is usually a low-yield procedure.

SMALPs embedding the β2-adrenergic receptor were prepared from a HEK293T cell line.

The ionic strength of buffers plays a key role in SMALP formation and isolation.

Standard SMALP protocols can be finely optimized to increase purification yields.

Graphical abstract
Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition
Authors: Lou Yue Clare , Olm Matthew R. , Diamond Spencer , Crits-Christoph Alexander , Firek Brian A. , Baker Robyn , Morowitz Michael J. , Banfield Jillian F.
Published: January 2021

Gut microbiome succession impacts infant development. However, it remains unclear what factors promote persistence of initial bacterial colonists in the developing gut. Here, we performed strain-resolved metagenomic analyses to compare gut colonization of preterm and full-term infants throughout the first year of life and evaluated links between strain persistence and strain origin as well as genetic potential. Analysis of 206 fecal metagenomes collected from full-term and preterm infants and their mothers revealed that infants’ initially distinct microbial communities converged by age one. Approximately 11% of early colonists, primarilyBacteroidesandBifidobacterium, persisted during the first year of life, and these were more prevalent in full-term compared to preterm infants. Gut-associated strains from mothers were significantly more likely to persist in the infant gut than other strains. Enrichment in genes for surface adhesion, iron acquisition and carbohydrate degradation may explain persistence of some strains through the first year of life.
Age, Origin, and Biogeography: Unveiling the Factors Behind the Diversification of Dung Beetles
Authors: Schwery Orlando , O’Meara Brian C.
Published: January 2021

The remarkable diversity and global distribution of dung beetles has long attracted the interest of researchers. However, there is still an ongoing debate on their origin, the reasons behind their diversity, and their path to global distribution. The two most prominent hypotheses regarding their origin and biogeographic history involve either vicariance events after the breakup of Gondwana, or an African origin and subsequent dispersal. One of the key reasons why the question is still disputed is a dependence on knowing the age of the dung beetles – a Mesozoic origin would favor the scenario of Gondwanan vicariance, a Cenozoic origin would suggest the out-of-Africa scenario. To help settle this longstanding question, we provide a taxonomically expanded phylogeny, with divergence times estimated under two calibration schemes suggesting an older or younger origin respectively. Using model-based inference, we estimate the ancestral area of the group and test for the influence of ranges on diversification rates. Our results support the hypothesis of an old age for Scarabaeinae and Gondwanan origin but remain ambiguous about the exact relation of range on lineage diversification.
Streptococcus suisencodes multiple allelic variants of a phase-variable Type III DNA methyltransferase, ModS, that control distinct phasevarions
Authors: Tram Greg , Jen Freda E.-C. , Phillips Zachary N. , Timms Jamie , Husna Asma-Ul , Jennings Michael P. , Blackall Patrick J. , Atack John M.
Published: January 2021

Streptococcus suisis a significant cause of bacterial meningitis in humans, particularly in S.E. Asia, and is a leading cause of respiratory and invasive disease in pigs. Phase-variable DNA methyltransferases, associated with Restriction-Modification (R-M) systems, are a source of epigenetic gene regulation, controlling the expression of multiple genes. These systems are known as phasevarions (phase-variable regulons), and have been characterised in many host-adapted bacterial pathogens. We recently described the presence of a Type III DNA methyltransferase inS. suis, ModS, which contains a simple sequence repeat (SSR) tract within the open reading frame of themodSgene, and which varied in length between individual strains. We also observed multiple allelic variants of themodSgene were present in a population ofS. suisisolates. Here, we demonstrate that a biphasic ON-OFF switching of expression occurs in the two most common ModS alleles, ModS1 and ModS2, and that switching is dependent on SSR tract length. Further, we show that ModS1 and ModS2 are active methyltransferases inS. suisusing Single-Molecule, Real Time (SMRT) sequencing. ON-OFF switching of each ModS allele results in the regulation of distinct phasevarions, with the ModS2 phasevarion impacting growth patterns and antibiotic resistance. This is the first demonstration of a phase-variable Type III DNA methyltransferase in a Gram-positive organism that controls a phasevarion. Characterising the phenotypic effects of phasevarions inS. suisis key to understanding pathogenesis and the development of future vaccines.

Importance

Streptococcus suisis a causative agent of meningitis, polyarthritis and polyserositis in swine, and is a major cause of zoonotic meningitis in humans. Here we investigate epigenetic gene regulation inS. suisby multiple phasevarions controlled by the phase-variable Type III DNA methyltransferase ModS. This is the first characterised example of a Type III R-M system regulating a phasevarion in a Gram-positive organism. We demonstrate that biphasic ON-OFF switching of ModS expression results in differences in bacterial growth and antibiotic resistance. Understanding the effects of ModS phase variation is required to determine the stably expressed antigenic repertoire ofS. suis, which will direct and inform the development of antimicrobial treatments and vaccines against this important pathogen.
Enhanced laterally resolved ToF-SIMS and AFM imaging of the electrically conductive structures in cable bacteria
Authors: Eachambadi Raghavendran Thiruvallur , Boschker Henricus T. S. , Franquet Alexis , Spampinato Valentina , Hidalgo-Martinez Silvia , Valcke Roland , Meysman Filip J. R. , Manca Jean V.
Published: January 2021

Cable bacteria are electroactive bacteria that form a long, linear chain of ridged cylindrical cells. These filamentous bacteria perform centimeter-scale long-range electron transport through parallel, interconnected conductive pathways of which the detailed chemical and electrical properties are still unclear. Here, we combine ToF-SIMS (time of flight secondary ion mass spectrometry) and AFM (atomic force microscopy) to investigate the structure and composition of this naturally-occurring electrical network. The enhanced lateral resolution achieved allows differentiation between the cell body and the cell-cell junctions that contain a conspicuous cartwheel structure. Three ToF-SIMS modes were compared in the study of so-called fiber sheaths (i.e., the cell material that remains after removal of cytoplasm and membranes and which embeds the electrical network). Among these, fast imaging delayed extraction (FI-DE) was found to balance lateral and mass resolution, thus yielding multiple benefits in the study of structure-composition relations in cable bacteria: (i) it enables the separate study of the cell body and cell-cell junctions, (ii) by combining FI-DE with in-situ AFM, the depth of Ni-containing protein – key in the electrical transport – is determined with greater precision, and (iii) this combination prevents contamination, which is possible when using an ex-situ AFM. Our results imply that the interconnects in extracted fiber sheaths are either damaged during extraction, or that their composition is different from fibers, or both. From a more general analytical perspective, the proposed methodology of ToF-SIMS in FI-DE-mode combined within-situAFM holds great promise for studying the chemical structure of other biological systems.
Spatiotemporal organization of BamA governs the pattern of outer membrane protein distribution in growingEscherichia colicells
Authors: Mamou Gideon , Inns Patrick G. , Sun Dawei , Kaminska Renata , Housden Nicholas G. , Cohen-Khait Ruth , Miller Helen , Storek Kelly M. , Rutherford Steven T. , Payandeh Jian , Kleanthous Colin
Published: January 2021

The outer membrane (OM) of Gram-negative bacteria is a robust protective barrier that excludes major classes of antibiotics. The assembly, integrity and functioning of the OM is dependent on β-barrel outer membrane proteins (OMPs), the insertion of which is catalyzed by BamA, the core component of the β-barrel assembly machine (BAM) complex. Little is known about BamA in the context of its native OM environment. Here, using high-affinity fluorescently-labelled antibodies in combination with diffraction-limited and super-resolution fluorescence microscopy, we uncover the spatial and temporal organization of BamA in liveEscherichia coliK-12 cells. BamA is clustered into ~150 nm diameter islands that contain an average of 10-11 BamA molecules, in addition to other OMPs, and are distributed throughout the OM and which migrate to the poles during growth. In stationary phase cells, BamA is largely confined to the poles. Emergence from stationary phase coincides with new BamA-containing islands appearing on the longitudinal axis of cells, suggesting they are not seeded by pre-existing BamAs but initiate spontaneously. Consistent with this interpretation, BamA-catalyzed OMP biogenesis is biased towards non-polar regions. Cells ensure the capacity for OMP biogenesis is uniformly distributed during exponential growth, even if the growth rate changes, by maintaining an invariant density of BamA-containing OMP islands (~9 islands/μm2) that only diminishes as cells enter stationary phase, the latter change governing what OMPs predominate as cells become quiescent. We conclude that OMP distribution inE. coliis driven by the spatiotemporal organisation of BamA which varies with the different phases of growth.

Significance

The integrity and functioning of the outer membrane (OM) of Gram-negative bacteria depends on the β-barrel assembly machinery (BAM). Although the structure and the mechanism of the complex have been widely explored, little information exists about the organization of the BAM complex and how it dictates protein distribution in the OM. Here, we utilized highly specific monoclonal antibodies to study the spatiotemporal organization of BamA, the key component of this complex. We reveal that BAM organization is dynamic and tightly linked to the cell’s growth phase. We further discover that the rate of BAM facilitated OMP biogenesis is significantly reduced near the poles. In turn, these features govern the biogenesis patterns and the distribution of OMPs on the cell surface.
Zinc supplement augments the suppressive effects of repurposed drugs of NF-kappa B inhibitor on ACE2 expression in human lung cell lines in vitro
Authors: Lee Ming-Cheng , Chen Yin-Kai , Hsu Yih-Jen , Lin Bor-Ru
Published: January 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a vast number of infections and fatalities worldwide. As the development and safety validation of effective vaccines are ongoing, drug repurposing is most efficient approach to search FDA approved agents against coronavirus disease 2019 (COVID-19). In the present study, we found that endogenous ACE2 expressions could be detected in H322M and Calu-3 cell lines, as well as their ACE2 mRNA and protein expressions were suppressed by pyrrolidine dithiocarbamate (PDTC), a NF-kappa B inhibitor, in dose- and time-dependent manners. Moreover, N-acetyl-cysteine (NAC) pretreatment reversed PDTC-induced ACE2 suppression, as well as the combined treatment of hydrogen peroxide and knockdown of p50 subunit of NF-kappa B by siRNA reduced ACE2 expression in H322M cells. In addition, anthelmintic drug triclabendazole and antiprotozoal drug emetine, repurposed drugs of NF-kappa B inhibitor, also inhibited ACE2 mRNA and protein expressions in H322M cells. Moreover, zinc supplement augmented the suppressive effects of triclabendazole and emetine on ACE2 suppression in H322M and Calu-3 cells. Taken together, these results indicate that ACE2 expression is modulated by reactive oxygen species (ROS) and NF-kappa B signal in human lung cell lines, and zinc combination with triclabendazole or emetine has the clinical potential for the prevention and treatment of COVID-19.
Fitness cost of vancomycin-resistantEnterococcus faeciumplasmids associated with hospital infection outbreaks
Authors: Tedim Ana P. , Lanza Val F. , Rodríguez Concepción M. , Freitas Ana R. , Novais Carla , Peixe Luísa , Baquero Fernando , Coque Teresa M.
Published: January 2021

Background

Vancomycin resistance is mostly associated withEnterococcus faeciumdue to Tn1546-vanAlocated on narrow- and broad-host plasmids of various families. The study’s aim was to analyse the effects of acquiring Tn1546-plasmids with proven epidemicity in different bacterial host backgrounds.

Methods

Widespread Tn1546-plasmids of different families RepA_N (n=5), Inc18 (n=4) and/or pHTβ (n=1), and prototype plasmids RepA_N (pRUM) and Inc18 (pRE25, pIP501) were analysed. Plasmid transferability and fitness cost were assessed usingE. faecium(GE1, 64/3) andEnterococcus faecalis(JH2-2/FA202/UV202) recipient strains. Growth curves (Bioscreen C) and Relative Growth Rates were obtained in presence/absence of vancomycin. Plasmid stability was analysed (300 generations). Whole genome sequencing (Illumina-MiSeq) of non-evolved and evolved strains (GE1/64/3 transconjugants, n=49) was performed. SNP calling (breseq software) of non-evolved strains was used for comparison.

Results

All plasmids were successfully transferred to differentE. faeciumclonal backgrounds. Most Tn1546-plasmids and Inc18 and RepA_N prototypes reduced host fitness (−2%-18%) while the cost of Tn1546expression varied according to the Tn1546-variant and the recipient strain (9-49%). Stability of Tn1546-plasmids was documented in all cases, often with loss of phenotypic resistance and/or partial plasmid deletions. Point mutations and/or indels associated with essential bacterial functions were observed on the chromosome of evolved strains, some of them linked to increased fitness.

Conclusions

The stability ofE. faeciumTn1546-plasmids in the absence of selective pressure and the high intra-species conjugation rates might explain the persistence of vancomycin resistance inE. faeciumpopulations despite the significant burden they might impose on bacterial host strains.
On the structural formula of smectites: a review and new data on the influence of exchangeable cations
Authors: García-Romero Emilia , Lorenzo Adrián , García-Vicente Andrea , Morales Juan , García-Rivas Javier , Suárez Mercedes
Published: January 2021

The understanding of the structural formula of smectite minerals is basic to predicting their physicochemical properties, which depend on the location of the cation substitutions within their 2:1 layer. This implies knowing the correct distribution and structural positions of the cations, which allows assigning the source of the layer charge of the tetrahedral or octahedral sheet, determining the total number of octahedral cations and, consequently, knowing the type of smectite. However, sometimes the structural formula obtained is not accurate. A key reason for the complexity of obtaining the correct structural formula is the presence of different exchangeable cations, especially Mg. Most smectites, to some extent, contain Mg2+ that can be on both octahedral and interlayer positions. This indeterminacy can lead to errors when constructing the structural formula. To estimate the correct position of the Mg2+ ions, that is their distribution over the octahedral and interlayer positions, it is necessary to substitute the interlayer Mg2+ and work with samples saturated with a known cation (homoionic samples). Seven smectites of the dioctahedral and trioctahedral types were homoionized with Ca2+, substituting the natural exchangeable cations. Several differences were found between the formulae obtained for the natural and Ca2+ homoionic samples. Both layer and interlayer charges increased, and the calculated numbers of octahedral cations in the homoionic samples were closer to four and six in the dioctahedral and trioctahedral smectites, respectively, with respect to the values calculated in the non-homoionic samples. This change was not limited to the octahedral sheet and interlayer, because the tetrahedral content also changed. For both dioctahedral and trioctahedral samples, the structural formulae improved considerably after homoionization of the samples, although higher accuracy was obtained the more magnesic and trioctahedral the smectites were. Additionally, the changes in the structural formulae sometimes resulted in changing the classification of the smectite.
A simulational study of the indirect-geometry neutron spectrometer BIFROST at the European Spallation Source, from neutron source position to detector position
Authors: Klausz M. , Kanaki K. , Kittelmann T. , Toft-Petersen R. , Birk J. O. , Olsen M. A. , Zagyvai P. , Hall-Wilton R. J.
Published: January 2021

The European Spallation Source (ESS) is intended to become the most powerful spallation neutron source in the world and the flagship of neutron science in upcoming decades. The exceptionally high neutron flux will provide unique opportunities for scientific experiments but also set high requirements for the detectors. One of the most challenging aspects is the rate capability and in particular the peak instantaneous rate capability, i.e. the number of neutrons hitting the detector per channel or cm2 at the peak of the neutron pulse. The primary purpose of this paper is to estimate the incident rates that are anticipated for the BIFROST instrument planned for ESS, and also to demonstrate the use of powerful simulation tools for the correct interpretation of neutron transport in crystalline materials. A full simulation model of the instrument from source to detector position, implemented with the use of multiple simulation software packages, is presented. For a single detector tube, instantaneous incident rates with a maximum of 1.7 GHz for a Bragg peak from a single crystal and 0.3 MHz for a vanadium sample are found. This paper also includes the first application of a new pyrolytic graphite model and a comparison of different simulation tools to highlight their strengths and weaknesses.
Inversion of explosive source land seismic data to determine source signature parameters
Authors: Ziolkowski Anton
Published: January 2021

In seismic land exploration, where terrain conditions limit the use of vibrator sources, explosive sources are the preferred choice, and in situations where low‐frequency energy is essential, explosive is the preferred source, because it contains energy down to DC (0 Hz). I present a new method to estimate the source time functions of explosion source seismic data, using a modified acquisition method, data processing, modelling and inversion. Two shots of different sizes are fired into the same geophone spread with source–receiver geometry arranged such that the Green's functions are essentially the same. The spectral ratio of corresponding seismic traces is then the spectral ratio of the source time functions. A corresponding synthetic ratio filter is calculated from Blake's explosion source model for the sources within each pair. Each modelled source is defined by five parameters: the minimum radius a of the elastic zone, the internal pressure p0 at a, the density of the rock ρ and two elastic constants for an isotropic rock, the P‐wave velocity c and Poisson's ratio σ. A grid search finds the source parameters that minimise the difference between the measured and synthetic filters for each source pair, thus yielding the two source time functions, but not their absolute amplitudes. Deconvolution of the shot records within each pair for the minimum‐phase source time functions recovers the estimated earth impulse response gathers, convolved only with the response of the recording system. The improved knowledge of the source signature is then helpful in subsequent processing, especially for reverse time migration, full waveform inversion and amplitude‐versus‐offset analysis. I consider shots at different depths in the same shot hole and shots at the same depth in different shot holes. The former configuration minimises differences in geophone coupling, and, in operations, quality control procedures must be met. There is considerable variation in recovered source parameters from place to place, caused by variations in charge size, soil or rock properties and source coupling.
Counsellors perceptions of the phenomenon of concentration difficulties
Authors: Hvidsten Bente Borthne , Valle Anne Marit
Published: January 2021

Pupils’ lack of concentration is a concern in everyday classrooms in Norway as in many other countries. Whereas research has defined different behaviour issues in classroom contexts, there has been less focus on how the counsellors, working at the Educational and Psychological Counselling Service (EPCS), describe different behaviour issues. This article is based on a study that aims to develop a deeper understanding of how the counsellors perceive the term ‘concentration difficulties’. Even though the term is widely used in templates and in national strategic documents to describe pupils’ disruptive behaviour, few other studies emphasise this perspective. The study has a phenomenological‐hermeneutic inspired approach and is based on individual in‐depth interviews with counsellors working at the EPCS. The key findings suggest that the counsellors understanding of the term are influenced by their personal perceptions of the term, their education and the way they facilitate adapted learning.
‘They have just given up on me’ How pupils labelled with social, emotional and behavioural difficulties (SEBD) experience the process of exclusion from school
Authors: Caslin Marie
Published: January 2021

For decades, the school exclusion rates have been a cause for concern within the English education system. We have witnessed a steady increase in the numbers of pupils being excluded since 2012. Evidence suggests that some children are more likely to be excluded from school, a significant number will have had the social, emotional and behavioural difficulties label attached to them. This article will draw on the work of Parsons and Howlett (Permanent exclusions from school: A case where society is failing its children. Support for Learning, 11, 3, 109–112, 1996) to see how much, if any, progress has been made since the publication of their work which raised concerns regarding the exclusion processes employed in England. Drawing on the perspectives of pupils, parents and teachers, 13 in‐depth case studies were developed, with emphasis placed on employing innovative and creative methods to hear the voices of young people. The findings revealed that young people, their parents and teachers feel the current education system continues to fail this group of young people.
Carl von Clausewitz and his Philosophy of War: The Evolution of a Reputation, 1831–2021
Authors: GERALD HUGHES R.
Published: January 2021

This article is concerned with the evolution of the reputation of the Prussian soldier and philosopher of war, Carl von Clausewitz (1780–1831). It examines developments in debates about the reception, and relevance, of Clausewitz's work for strategic thought in both the historical and contemporary contexts. This article takes note of many of the misperceptions and misinterpretations directed at Clausewitz's work since his death. It argues that much of the criticism directed at Clausewitz is rooted in a visceral dislike of past proponents of Clausewitz for their aggressive and militaristic policies. An appreciation of this history is nevertheless useful for facilitating accurate interpretations of Clausewitz's work. Finally, the article argues that the notion of Clausewitz as advocate of militarism and aggressive war has been largely discredited. Indeed, in today's Federal Republic of Germany, the reformers masterminding the Wars of Liberation against Napoleon, of whom Clausewitz was one, and the resistance involved in the bomb plot of 20 July 1944, have now come to represent a useable historical tradition.
State of the Field: Material Culture
Authors: DYER SERENA
Published: January 2021

This article surveys the state of the field of material culture within the discipline of history. The study of material culture – the myriad layers of cultural meaning embedded within objects – has been adopted by historians from colleagues in anthropology, archaeology and museum studies, and continues to thrive as an interdisciplinary field in tandem with art history and literary studies. As inventive digital and embodied methodologies within material culture begin to shape the future of the field, this article takes the opportunity to reflect upon the opportunities and impediments presented to scholars of material culture. It elucidates the diverse and often unfamiliar vernaculars of material objects, and reflects upon future directions in the study of material culture.
The associations of medical marijuana policies with opioid‐related health care utilization
Authors: Jayawardhana Jayani , Fernandez Jose M.
Published: January 2021

Objective

To examine the associations between medical marijuana policies and opioid‐related hospitalizations and emergency department visits.

Data Sources

We utilized quarterly rates of hospital discharge data from the Healthcare Cost and Utilization Project's (HCUP) Fast Stats Database from 2005 to 2016 along with state‐level sociodemographic data from US Census Bureau and Bureau of Labor Statistics and opioid‐related state health policy data from publicly available sources for the analysis.

Study Design

Analyses were carried out using a difference‐in‐differences regression approach. We estimate heterogeneous effects of medical marijuana policies such as initial policy, presence of active dispensary, and home cultivation on opioid‐related hospitalizations and emergency department visits related to opioids.

Data Collection/Extraction Methods

Publicly available secondary data were collected, linked, and analyzed. Observations with missing values for explanatory variables were excluded from the analysis.

Principal Findings

Regression results indicate that type of medical marijuana policy has varying effects on opioid‐related hospitalizations and emergency department visits. States that allow home cultivation of medical marijuana experienced significant positive associations with opioid‐related hospitalizations and emergency department visits, while no effect was observed with medical marijuana dispensaries. Moreover, recreational marijuana policies were positively associated with opioid‐related hospitalizations.

Conclusions

The findings indicate that the effects of medical marijuana policies on opioid‐related hospitalizations and emergency department visits vary depending on the type of medical marijuana policy. Our findings indicate that the implementation of home cultivation of marijuana is positively associated with hospitalizations and emergency department visits related to opioids, suggesting that easier access to marijuana among opioid users may result in adverse health conditions that need treatment.
Access block in Australian emergency departments 2017–2020
Authors: Richardson Drew B
Published: January 2021

Objective

To describe Australian ED workload over the period 2017–2020 using data from twice annual Access Block Point Prevalence Studies, and to identify any impact of the COVID‐19 pandemic.

Methods

Retrospective analysis of demand and occupancy data provided by the Australasian College for Emergency Medicine accredited EDs in voluntary surveys at the start of June and September 2017–2020. Hospitals answering all surveys were grouped and compared by jurisdiction and role delineation.

Results

A total of 121 EDs were eligible, 63% supplied complete occupancy data and 53% complete demand data. Between the June 2017 and 2019 surveys, mean daily ED presentations increased by 11.4% (P= 0.0003). The number being treated at 10.00 hours rose by 27.7% (P< 0.0001) and those experiencing access block (waiting for an inpatient bed, been in ED more than 8 h) rose by 46.1% (P= 0.001). Between the June 2019 and 2020 surveys, ED presentations fell by an average of 12.6% (P< 0.0001), ward admissions were almost unchanged (−6.0%,P= NS), and patients who did not wait to be seen fell by 57.8% (P< 0.0001). Major Paediatric Referral hospitals reported a 28% decrease in presentations. By September 2020, only the state of Victoria (ongoing state of emergency) and Major Paediatric Referral hospitals reported demand lower than 2019 or occupancy lower than 2018.

Conclusions

Occupancy increased by more than demand 2017–2019, with some decrease in 2020: in June presentations were 12.7% lower than 2019, in September back to the normal range outside Victorian and Major Paediatric Referral hospitals. Future research needs to consider locality, role delineation and work practice change in comparing ED pandemic responses.
Juvenoids on aphids to prolong optimal stages
Authors: Lai Rongquan , Bai Jingjing , Gu Gang , Zhou Ting , Mi Yuee , Zhang Bang , Han Meng , Bai Jianbao
Published: January 2021

In recent years, Aphidius gifuensis, a critical parasitoid, has been increasingly used to control Myzus persicae in tobacco. However, problems due to inconsistent emergence and insufficient numbers of A. gifuensis to control M. persicae have arisen in artificial reproduction. Here, we investigated the effects of the juvenoids ZR‐512, ZR‐777, ZR‐515, fenoxycarb and juvenile hormone (JH) III on the performance of M. persicae, the activities of molting enzymes and parasitism rates. The aim was to identify juvenoids that may prolong the ‘arrived too early’ optimal stages of M. persicae for A. gifuensis parasitism to address the problems mentioned above. The results showed that the developmental durations of 2nd‐ and 3rd‐instar nymphs of the parental (F0) and offspring (F1) generations of M. persicae were significantly prolonged by juvenoid treatment. The instar durations ranged from 4.00 to 13.67 h for the parental generation and from 8.00 to 32.00 h for the offspring. M. persicae lifespan was not significantly affected by the juvenoids, whereas fecundity was. Additionally, the phenoloxidase and chitinase contents and activities in M. persicae were significantly reduced by the juvenoids, whereas the parasitism rate of A. gifuensis on M. persicae was unaffected. Our study provides information that can help prolong the ‘arrived too early’ period of effective parasitism of M. persicae nymphs by A. gifuensis and thereby benefit the large‐scale artificial reproduction of A. gifuensis. These findings will enhance the biological control of M. persicae and highlight the mechanism by which juvenoids affect M. persicae development by regulating phenoloxidase or chitinase.
Tonsillitis as a possible predisposition to synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) syndrome
Authors: Xiang Yirong , Wang Yutong , Cao Yihan , Li Zhaohui , Xiong Dingkun , Wang Lun , Zhang Wen , Zeng Xiaofeng , Wang Yi , Li Chen
Published: January 2021

Aim

To present the prevalence of tonsillitis in synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) patients, to compare the clinical characteristics and disease activities between SAPHO patients with and without tonsillitis and to preliminarily explore the efficacy of tonsillectomy in SAPHO syndrome.

Method

A total of 58 SAPHO patients were included. Clinical data were collected, including demographic characteristics and acute phase reactants (erythrocyte sedimentation rate, high‐sensitivity C‐reactive protein). The visual analog scale (VAS), Palmoplantar Pustule Psoriasis Area Severity Index (PPPASI) and Nail Psoriasis Severity Index (NAPSI) were used to measure the severity of bone pain, skin lesions and nail lesions, respectively. Patients were referred to the otolaryngology department for tonsil examinations, including tonsil hypertrophy (grade ≥ 2), chronic congestion, inflammatory secretion and tonsil stones. The patients who underwent tonsillectomy were followed up after the surgery.

Results

A total of 67.2% of patients had tonsillitis. Patients with tonsillitis had markedly higher PPPASI (1.2 [0, 7.4] vs. 7.6 [1.75, 15.5], P = .018) and NAPSI (0 [0, 21] vs. 8 [3, 28], P = .032) scores. After tonsillectomy, the patients experienced significantly improved bone pain (VAS, 5 [4, 7] vs. 3 [1, 4], P = .034) and skin lesions (PPPASI, 16.2 [7.05, 18.35] vs 1.8 [0.7, 3.7], P = .028).

Conclusion

Approximately 2/3 of SAPHO patients had tonsillitis. Patients with tonsillitis had more severe skin and nail lesions. Tonsillectomy might be associated with improved bone and skin symptoms in SAPHO patients. Future prospective controlled studies are warranted.