bluuebunny/crossref_metadata_2025 huggingface dataset:
Generation of Super-resolution Images from Barcode-based Spatial Transcriptomics Using Deep Image Prior
Authors: Park Jeongbin , Cook Seungho , Lee Dongjoo , Choi Jinyeong , Yoo Seongjin , Im Hyung-Jun , Lee Daeseung , Choi Hongyoon
Published: June 2023

Spatial transcriptomics (ST) has revolutionized the field of biology by providing a powerful tool for analyzing gene expressionin situ. However, current ST methods, particularly barcode-based methods, have limitations in reconstructing high-resolution images from barcodes sparsely distributed in slides. Here, we present SuperST, a novel algorithm that enables the reconstruction of dense matrices from low-resolution ST libraries. SuperST based on deep image prior reconstructs spatial gene expression patterns as image matrices. SuperST allows gene expression mapping to better reflect immunofluorescence (IF) images. Compared with previous methods, SuperST generated output images that more closely resembled IF images for given gene expression maps. Additionally, SuperST overcomes the limitations inherent in IF images, highlighting its potential applications in the realm of spatial biology. By providing a more detailed understanding of gene expressionin situ, SuperST has the potential to contribute to comprehensively understanding biology from various tissues.
A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and asymptomatic bacteria
Authors: Flores Carlos , Ling Jefferson , Loh Amanda , Maset Ramón Garcia , Aw Angeline , White Ian J. , Fernando Raymond , Rohn Jennifer L.
Published: June 2023

Urinary tract infection is among the most common infections worldwide, and is typically studied in animals and cell lines with limited uropathogenic strains. Here, we assessed diverse bacterial pathogens and asymptomatic bacteria (ASB) in a human urothelial microtissue model including full stratification/differentiation and urine tolerance. Several uropathogens and ASB-likeE. coliinvaded intracellularly, suggesting invasion is a shared survival strategy, instead of a virulence hallmark. TheE. coliadhesin FimH was required for intracellular community formation, but not for invasion. Other shared lifestyles included filamentation (Gram-negatives), chaining (Gram-positives) and hijacking of exfoliating cells, while biofilm-like aggregates formed mainly withPseudomonasandProteus. Urothelial cells expelled invasive bacteria in Rab-/LC3-decorated structures, while highly cytotoxic/invasive uropathogens, but not ASB, disrupted host barrier function and strongly induced exfoliation and cytokine production. Overall, this work highlights diverse species-/strain-specific infection strategies and corresponding host responses in a human urothelial microenvironment, providing insights at the tissue, cell and molecular level.

One-Sentence Summary

A human urothelial model revealed shared colonization strategies between uropathogens and asymptomatic bacteria, and pathogen-specific innate immune responses
Variations in Homoeologous Dosage and Epigenomics Mark the Early Evolution of SyntheticBrassicaTetraploids
Authors: Zhang Kang , Yang Yinqing , Zhang Lei , Cui Yinan , Wu Jian , Liang Jianli , Li Xing , Zhang Lingkui , Zhang Xin , Zhang Yiyue , Guo Zhongwei , Chen Shumin , Freeling Michael , Wang Xiaowu , Cheng Feng
Published: June 2023

Polyploidization is important in plant evolution and is becoming increasingly important in crop breeding and material creation. Studies have provided evidence for structural variations and epigenomic repatterning in synthetic polyploidizations, but the relationships between structural and epigenomic variations, as well as their effects on gene expression and phenotypic variations are unknown. Here, we investigated the genome-wide large deletion/duplication regions (DelDups) and genomic methylation dynamics, in the leaf organ as a representative, of progenies from eight generations that derived from the synthetic tetraploidization betweenBrassica rapaandBrassica oleracea. We found that half or complete deletion/duplication of fragments ranging in size from 400 kb to 65.85 Mb, with a mean size of 5.70 Mb, occurred frequently from the first generation of selfing and thereafter. The genes located in these DelDups expressed at levels expected for a positive dosage effect, as indicated by the positive association between expression and the copy number of these genes. Plants containing these DelDups also showed distinct phenotypic variations. The whole genome methylation level experienced significant fluctuations in different generations and eventually decreased in the latter generations. Moreover, the DelDups did not show methylation changes from other individuals of the same generation, and the local regions with methylation alterations did not affect gene expression. Our findings provide new insights into the early evolution of polyploid genomes and guide the use of synthetic polyploidizations in breeding.
Metabolic-Pathway-Presence-Heatmap (MPPH): Constructing phylogenetic trees based on metabolic pathways
Authors: Du Yi-Heng , Mu Jing-Hua
Published: June 2023

Genome sequencing has revolutionized the study of biological systems, enabling exploration of species origins, evolution, and identification. However, traditional methods for constructing phylogenetic trees based on raw sequence data require substantial computational resources and may be challenging for biologists with limited computer knowledge. To address this, a lightweight tree-building tool was developed, Metabolic-Pathway-Presence-Heatmap (MPPH), leveraging Python programming and the KEGG metabolomics database to construct phylogenetic trees based on metabolic pathway information. This approach reduces computational and time requirements while focusing the analysis on metabolic pathways. The tool provides a rapid and reliable option for biologists to investigate the evolutionary and taxonomic aspects of species. Additionally, the tool incorporates a heatmap feature, allowing users to visualize the presence or absence of metabolic pathways across multiple species. The code is available athttp://github.com/DeweyYihengDu/Metabolic-Pathway-Presence-Heatmap.
E2F1 methylation by SETD6 regulates SETD6 expression via positive feedback mechanism
Authors: Kublanovsky Margarita , Ulu Gizem T. , Weirich Sara , Levy Nurit , Feldman Michal , Jeltsch Albert , Levy Dan
Published: June 2023

The protein lysine methyltransferase SETD6 has been shown to influence different cellular activities and are critically involved in the regulation of diverse developmental and pathological processes. However, the upstream signal which regulates the mRNA expression of SETD6 is not known. Bioinformatics analysis revealed that SETD6 promoter has a binding site for the transcription factor E2F1. Using various experimental systems, we confirmed that E2F1 binds to the SETD6 promoter and regulates SETD6 mRNA expression. Our further observation that this phenomenon is SETD6 dependent, suggested that SETD6 and E2F1 are linked. We next demonstrate that SETD6 mono-methylates E2F1 specifically at K117in-vitroand in cells. Finally, we show that E2F1 methylation at K117 positively regulates the expression level of SETD6 mRNA. Depletion of SETD6 or overexpression of E2F1 K117R mutant which canot be methylated by SETD6, reverses the effect. Taken together, our data provide evidence for a positive feedback mechanism which regulates the expression of SETD6 by E2F1 in a SETD6 methylation dependent manner and highlight the importance of protein lysine methyltransferases and lysine methylation signaling in the regulation of gene transcription.
Unique vulnerability ofRAC1-mutant melanoma to combined inhibition of CDK9 and immune checkpoints
Authors: Cannon Alexa C. , Budagyan Konstantin , Uribe-Alvarez Cristina , Kurimchak Alison M. , Araiza-Olivera Daniela , Cai Kathy Q. , Peri Suraj , Zhou Yan , Duncan James S. , Chernoff Jonathan
Published: June 2023

RAC1P29Sis the third most prevalent hotspot mutation in sun-exposed melanoma.RAC1alterations in cancer are correlated with poor prognosis, resistance to standard chemotherapy, and insensitivity to targeted inhibitors. AlthoughRAC1P29Smutations in melanoma andRAC1alterations in several other cancers are increasingly evident, the RAC1-driven biological mechanisms contributing to tumorigenesis remain unclear. Lack of rigorous signaling analysis has prevented identification of alternative therapeutic targets forRAC1P29S-harboring melanomas. To investigate the RAC1P29S-driven effect on downstream molecular signaling pathways, we generated an inducible RAC1P29Sexpression melanocytic cell line and performed RNA-sequencing (RNA-seq) coupled with multiplexed kinase inhibitor beads and mass spectrometry (MIBs/MS) to establish enriched pathways from the genomic to proteomic level. Our proteogenomic analysis identified CDK9 as a potential new and specific target in RAC1P29S-mutant melanoma cells.In vitro, CDK9 inhibition impeded the proliferation of in RAC1P29S-mutant melanoma cells and increased surface expression of PD-L1 and MHC Class I proteins.In vivo, combining CDK9 inhibition with anti-PD-1 immune checkpoint blockade significantly inhibited tumor growth only in melanomas that expressed the RAC1P29Smutation. Collectively, these results establish CDK9 as a novel target in RAC1-driven melanoma that can further sensitize the tumor to anti-PD-1 immunotherapy.
Loss ofBacteroides thetaiotaomicronbile acid altering enzymes impact bacterial fitness and the global metabolic transcriptome
Authors: McMillan Arthur S. , Foley Matthew H. , Perkins Caroline E. , Theriot Casey M.
Published: June 2023

Bacteroides thetaiotaomicron(B. theta) is a Gram-negative gut bacterium that encodes enzymes that alter the bile acid pool in the gut. Primary bile acids are synthesized by the host liver and are modified by gut bacteria.B. thetaencodes two bile salt hydrolases (BSHs), as well as a hydroxysteroid dehydrogenase (HSDH). We hypothesize thatB. thetamodifies the bile acid pool in the gut to provide a fitness advantage for itself. To investigate each gene’s role, different combinations of genes encoding bile acid altering enzymes (bshA, bshB, andhsdhA) were knocked out by allelic exchange, including a triple KO. Bacterial growth and membrane integrity assays were done in the presence and absence of bile acids. To explore ifB. theta’sresponse to nutrient limitation changes due to the presence of bile acid altering enzymes, RNASeq analysis of WT and triple KO strains in the presence and absence of bile acids was done. WTB. thetais more sensitive to deconjugated bile acids (CA, CDCA, and DCA) compared to the triple KO, which also decreased membrane integrity. The presence ofbshBis detrimental to growth in conjugated forms of CDCA and DCA. RNA-Seq analysis also showed bile acid exposure impacts multiple metabolic pathways inB. theta, but DCA significantly increases expression of many genes in carbohydrate metabolism, specifically those in polysaccharide utilization loci or PULs, in nutrient limited conditions. This study suggests that bile acidsB. thetaencounters in the gut may signal the bacteria to increase or decrease its utilization of carbohydrates. Further study looking at the interactions between bacteria, bile acids, and the host may inform rationally designed probiotics and diets to ameliorate inflammation and disease.

Importance

Recent work on BSHs in Gram-negative bacteria, such asBacteroides, has primarily focused on how they can impact host physiology. However, the benefits bile acid metabolism confers to the bacterium that performs it is not well understood. In this study we set out to define if and howB. thetauses its BSHs and HSDH to modify bile acids to provide a fitness advantage for itselfin vitroandin vivo. Genes encoding bile acid altering enzymes were able to impact howB. thetaresponds to nutrient limitation in the presence of bile acids, specifically carbohydrate metabolism, affecting many polysaccharide utilization loci (PULs). This suggests thatB. thetamay be able to shift its metabolism, specifically its ability to target different complex glycans including host mucin, when it comes into contact with specific bile acids in the gut. This work will aid in our understanding of how to rationally manipulate the bile acid pool and the microbiota to exploit carbohydrate metabolism in the context of inflammation and other GI diseases.
Eukaryotic antiviral immune proteins arose via convergence, horizontal transfer, and ancient inheritance
Authors: Culbertson Edward M. , Levin Tera C.
Published: June 2023

Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to anti-phage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for three innate immune families (CD-NTases [including cGAS], STINGs, and Viperins) by deeply sampling protein diversity across eukaryotes. We find that Viperins and OAS family CD-NTases are truly ancient immune proteins, likely inherited since the last eukaryotic common ancestor and possibly longer. In contrast, we find other immune proteins that arose via at least four independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while two more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the Mab21 superfamily (containing cGAS) which has diversified via a series of animal-specific duplications, and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STINGs arising via convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial anti-phage genes.
Decreased efficacy of a COVID-19 vaccine due to mutations present in early SARS-CoV-2 variants of concern
Authors: Weidenbacher Payton A.-B. , Friedland Natalia , Sanyal Mrinmoy , Morris Mary Kate , Do Jonathan , Hanson Carl , Kim Peter S.
Published: June 2023

With the SARS-CoV-2 virus still circulating and evolving, there remains an outstanding question if variant-specific vaccines represent the optimal path forward, or if other strategies might be more efficacious towards providing broad protection against emerging variants. Here, we examine the efficacy of strain-specific variants of our previously reported, pan-sarbecovirus vaccine candidate, DCFHP-alum, a ferritin nanoparticle functionalized with an engineered form of the SARS-CoV-2 spike protein. In non-human primates, DCFHP-alum elicits neutralizing antibodies against all known VOCs that have emerged to date and SARS-CoV-1. During development of the DCFHP antigen, we investigated the incorporation of strain-specific mutations from the major VOCs that had emerged to date: D614G, Epsilon, Alpha, Beta, and Gamma. Here, we report the biochemical and immunological characterizations that led us to choose the ancestral Wuhan-1 sequence as the basis for the final DCFHP antigen design. Specifically, we show by size exclusion chromatography and differential scanning fluorimetry that mutations in the VOCs adversely alter the antigen’s structure and stability. More importantly, we determined that DCFHP without strain-specific mutations elicits the most robust, cross-reactive response in both pseudovirus and live virus neutralization assays. Our data suggest potential limitations to the variant-chasing approach in the development of protein nanoparticle vaccines, but also have implications for other approaches including mRNA-based vaccines.
SETDB1 modulates the TGFβ response in Duchenne muscular dystrophy myotubes
Authors: Granados Alice , Zamperoni Maeva , Rapone Roberta , Moulin Maryline , Boyarchuk Ekaterina , Bouyioukos Costas , Maestro Laurence Del , Joliot Véronique , Negroni Elisa , Mohamed Myriame , Piquet Sandra , Bigot Anne , Grand Fabien Le , Albini Sonia , Ait-Si-Ali Slimane
Published: June 2023

Overactivation of the TGFβ signaling in Duchenne muscular dystrophy (DMD) is a major hallmark of disease progression, leading to fibrosis and muscle dysfunction. Here, we investigated the role of SETDB1, a histone lysine methyltransferase involved in muscle differentiation. Our data show that, following TGFβ induction, SETDB1 accumulates in the nuclei of healthy myotubes, while being already present in the nuclei of DMD myotubes where TGFβ signaling is constitutively activated. Interestingly, transcriptomics revealed that depletion of SETDB1 in DMD myotubes leads to downregulation of TGFβ-target genes coding for secreted factors involved in extracellular matrix remodeling and inflammation. Consequently, SETDB1 silencing in DMD myotubes abrogates the deleterious effect of their secretome on myoblast differentiation by impairing myoblast pro-fibrotic response. Our findings indicate that SETDB1 potentiates the TGFβ-driven fibrotic response in DMD muscles, providing a new axis for therapeutic intervention.

Key results

TGFβ induces nuclear accumulation of SETDB1 in healthy myotubes

SETDB1 is enriched in DMD myotube nuclei with intrinsic TGFβ pathway overactivation

SETDB1 LOF in DMD myotubes attenuates TGFβ-induced pro-fibrotic response

Secretome of TGFβ-treated DMD myotubes with SETDB1 LOF is less deleterious on myoblast differentiation
Analysis of the economic effect of RCEP under the “Indo-Pacific strategy”: the GTAP model
Authors: Pan Su , Zhang Xuanhao , Bhuiyan Miraj Ahmed
Published: June 2023

Purpose

This study reveals the economic impact of the Indo-Pacific Strategy on the Regional Comprehensive Economic Partnership (RCEP).

Design/methodology/approach

This paper uses the GTAP model to analyze the economic effects of RCEP under the effect of the “Indo-Pacific Strategy” under different scenarios.

Findings

The results show that (1) with the improvement of the implementation effect of the US “Indo-Pacific Strategy,” the welfare level of China has gradually had a significant negative impact, while the welfare level of US Allies and partners has been further improved. (2) The implementation of the Indo-Pacific Strategy will further expand the import scale of Japan, South Korea and other Allies that are both RCEP members and the USA and slightly reduce the import scale of the European Union (EU) and other countries. (3) After the USA implemented the “Indo-Pacific Strategy,” its export scale has significantly improved, and it has been able to completely offset the adverse effects of the signing of RCEP on its exports. China's export scale has also gradually declined, and Japan has benefited the most.

Originality/value

There are three main possible contributions to this article: first, the authors combined geopolitical factors to simulate and evaluate the economic effects of RCEP under different Indo-Pacific Strategy implementation scenarios, which is more relevant than analyzing the economic effects of RCEP in a “vacuum.” Second, the standard static GTAP model can only measure the change of equilibrium state before and after the trade policy. At the same time, the dynamic GTAP model (GTAP-Dyn) introduces mechanisms such as capital flow and capital accumulation and treats time as a continuous variable affected by exogenous variables so that each variable has a time dimension so as better to simulate the medium- and long-term economic effects. This paper refers to the dynamic recursion method of Walmsley (2006) and Yang (2011) to update the base year of the GTAP version 10.0 database to 2020, that is the time when RCEP officially reached 2020. The simulation results of shock variables introduced into the baseline scenario are more reliable. Third, the authors analyze the welfare effect of RCEP and the impact on the import and export of relevant countries from the macrolevel and examine the impact on different products in different countries from the microlevel.
Smart tourism in the Baltic states: current developments and trends
Authors: Litavniece Lienite , Lonska Jelena , Zvaigzne Anda , Wieda Nina , Adamoniene Rūta
Published: June 2023

Purpose

The purpose of this paper is to evaluate and compare the current trends in development of the second largest cities in each Baltic state – Tartu (Estonia), Kaunas (Lithuania), and Daugavpils (Latvia) – as smart destinations, based on publicly available tourism information.

Design/methodology/approach

The study uses a case study employing a descriptive research method, and the authors reached their conclusions based on this material. Furthermore, the paper primarily focuses on literature and new research which deals with tourism in the 21st century, its innovations, changes, and trends.

Findings

The levels and directions of development of Tartu, Kaunas, and Daugavpils as a smart tourism destination are different. Although all three are the second largest cities in each Baltic State, their initial historical development, availability of resources, locations, and strategic development of the country show differences in development. Tartu conforms to the standards in all four categories. However, the category of digitalization receives the most attention and contributes to the positive smart destination result in the other three categories. Comparatively, Daugavpils records fewer current achievements according to the STDC, although the authors believe that there is potential that can be seen in the strategic policy documents. However, judging by all four categories, Daugavpils, similarly to Kaunas, currently demonstrates the greatest achievements in the culture heritage and creativity category.

Originality/value

This paper presents data and compares smart tourism development trends in the second largest cities in each Baltic country.
Worldviews about change: Their structure and their implications for understanding responses to sustainability, technology, and political change
Authors: Bain Paul G. , Bongiorno Renata , Tinson Kellie , Heanue Alanna , Gómez Ángel , Guan Yanjun , Lebedeva Nadezhda , Kashima Emiko , González Roberto , Chen Sylvia Xiaohua , Blumen Sheyla , Kashima Yoshihisa
Published: June 2023

People hold different perspectives about how they think the world is changing or should change. We examined five of these “worldviews” about change: Progress, Golden Age, Endless Cycle, Maintenance, and Balance. In Studies 1–4 (total N = 2733) we established reliable measures of each change worldview, and showed how these help explain when people will support or oppose social change in contexts spanning sustainability, technological innovations, and political elections. In mapping out these relationships we identify how the importance of different change worldviews varies across contexts, with Balance most critical for understanding support for sustainability, Progress/Golden Age important for understanding responses to innovations, and Golden Age uniquely important for preferring Trump/Republicans in the 2016 US election. These relationships were independent of prominent individual differences (e.g., values, political orientation for elections) or context‐specific factors (e.g., self‐reported innovativeness for responses to innovations). Study 5 (N = 2140) examined generalizability in 10 countries/regions spanning five continents, establishing that these worldviews exhibited metric invariance, but with country/region differences in how change worldviews were related to support for sustainability. These findings show that change worldviews can act as a general “lens” people use to help determine whether to support or oppose social change.
La migration interprovinciale chez les immigrants musulmans : La francophonie comme vecteur d'intégration?
Authors: Legault‐Leclair Jacob
Published: June 2023

Au Canada, les immigrants sont plus susceptibles de migrer à l'intérieur du pays—lors de migrations interprovinciales par exemple—que les individus nés au Canada. C'est notamment le cas des immigrants musulmans. Dans cet article, nous cherchons à identifier les caractéristiques déterminantes pour les secondes migrations entreprises par ces immigrants. Pour ce faire, nous avons posé notre regard sur (1) les caractéristiques sociodémographiques propres à cette communauté (la langue en particulier) et (2) au contexte sociopolitique des différentes provinces accueillant ces immigrants. Les résultats nous poussent à relativiser l'hypothèse d'une tension entre le fait d'habiter un milieu francophone au contexte sociopolitique tendu pour la communauté musulmane et un milieu anglophone où les enjeux sociopolitiques propres à cette communauté sont moins présents. Au‐delà des considérations strictement économiques, les immigrants musulmans doivent également négocier leur intégration en tenant compte de la langue et du milieu où certains enjeux sociopolitiques les concernant sont plus ou moins débattus et/ou un milieu où leur langue officielle de choix n'est pas parlée.
Sensitivity of tropical montane birds to anthropogenic disturbance and management strategies for their conservation in agricultural landscapes
Authors: Ausprey Ian J. , Newell Felicity L. , Robinson Scott K.
Published: June 2023

Tropical montane bird communities are hypothesized to be highly sensitive to anthropogenic disturbance because species are adapted to a narrow range of environmental conditions and display high rates of endemism. We assessed avian sensitivity at regional and continental scales for a global epicenter of montane bird biodiversity, the tropical Andes. Using data from an intensive field study of cloud forest bird communities across 7 landscapes undergoing agricultural conversion in northern Peru (1800–3100 m, 2016–2017) and a pan‐Andean synthesis of forest bird sensitivity, we developed management strategies for maintaining avian biodiversity in tropical countrysides and examined how environmental specialization predicts species‐specific sensitivity to disturbance. In Peru, bird communities occupying countryside habitats contained 29–93% fewer species compared with those in forests and were compositionally distinct due to high levels of species turnover. Fragments of mature forest acted as reservoirs for forest bird diversity, especially when large or surrounded by mixed successional vegetation. In high‐intensity agricultural plots, an addition of 10 silvopasture trees or 10% more fencerows per hectare increased species richness by 18–20%. Insectivores and frugivores were most sensitive to disturbance: abundance of 40–70% of species declined in early successional vegetation and silvopasture. These results were supported by our synthesis of 816 montane bird species studied across the Andes. At least 25% of the species declined due to all forms of disturbance, and the percentage rose to 60% in agricultural landscapes. The most sensitive species were those with narrow elevational ranges and small global range sizes, insectivores and carnivores, and species with specialized trophic niches. We recommend protecting forest fragments, especially large ones, and increasing connectivity through the maintenance of early successional vegetation and silvopastoral trees that increase avian diversity in pastures. We provide lists of species‐specific sensitivities to anthropogenic disturbance to inform conservation status assessments of Andean birds.
International survey of cytopathology training during the pandemic: Water under the bridge?
Authors: Piletska Nataliya
Published: June 2023

The purpose of this study was to assess the impact of the COVID‐19 pandemic on cytopathology training at an international level. An anonymous online questionnaire was distributed by members of the international cytopathological community to medical practitioners in cytopathology. The survey explored perceived changes in cytology workload and workflow during the pandemic, and its effect on both non‐cervical and cervical cytology reporting and teaching. A total of 82 responses were received from seven countries. Approximately half of the respondents reported a decrease in the number and range of cytology cases during the pandemic. Nearly half (47%) saw a reduction in the opportunity to co‐report with consultants/attendings, and 72% of the respondents reported that their consultants/attendings were working remotely during the pandemic. Another 34% of the respondents were redeployed for 3 weeks to 1 year, with 96% stating that this period was only partially compensated for during their training, if at all. The pandemic negatively affected the opportunity to report cervical cytology, perform fine needle aspirations, and participate in multidisciplinary team meetings. Most respondents (69%) saw a decrease in the amount and quality (52%) of face‐to‐face departmental cytology teaching, whereas remote departmental teaching improved in amount (54%) and quality (49%). Almost half (49%) reported that cytology teaching in the regional, national, and international settings increased in both amount and quality. The pandemic catalysed many changes in cytopathology training, affecting the trainees' exposure to cases, the use of remote reporting, consultant/attending working practices, redeployment, and local as well as external teaching.
Views on minimum unit pricing for alcohol before its introduction among people with alcohol dependence in Scotland: A qualitative interview study
Authors: Hughes Jane , Livingston Wulf , Buykx Penny , Johnston Allan , Little Simon , McCarthy Trevor , McLean Alex , Perkins Andy , Wright Alex , Holmes John
Published: June 2023

Introduction

Scotland implemented a minimum price per unit of alcohol (MUP) of £0.50 in May 2018 (1 UK unit = 10 mL/8 g ethanol). Some stakeholders expressed concerns about the policy having potential negative consequences for people with alcohol dependence. This study aimed to investigate anticipated impacts of MUP on people presenting to alcohol treatment services in Scotland before policy implementation.

Methods

Qualitative interviews were conducted with 21 people with alcohol dependence accessing alcohol treatment services in Scotland between November 2017 and April 2018. Interviews examined respondents' current and anticipated patterns of drinking and spending, effects on their personal life, and their views on potential policy impact. Interview data were thematically analysed using a constant comparison method.

Results

Three key themes were identified: (i) strategies used to manage the cost of alcohol and anticipated responses to MUP; (ii) broader effects of MUP; and (iii) awareness and preparedness for MUP. Respondents expected to be impacted by MUP, particularly those on low incomes and those with more severe dependence symptoms. They anticipated using familiar strategies including borrowing and reprioritising spending to keep alcohol affordable. Some respondents anticipated negative consequences. Respondents were sceptical about the short‐term benefits of MUP for current drinkers but felt it might prevent harm for future generations. Respondents had concerns about the capacity of treatment services to meet support needs.

Discussion and conclusions

People with alcohol dependence identified immediate concerns alongside potential long‐term benefits of MUP before its introduction. They also had concerns over the preparedness of service providers.
Educational Institutions and Indoctrination
Authors: Martin Christopher
Published: June 2023

The concept of indoctrination is typically used to characterize the actions of individual educators. However, it has become increasingly common for citizens to raise concerns about the indoctrinatory effects of institutions such as schools and universities. Are such worries fundamentally misconceived, or might some state of affairs obtain under which it can be rightly said that an educational institution is engaged in indoctrination? In this paper Christopher Martin outlines what the concept of institutional indoctrination could mean. He then uses Jürgen Habermas's discourse theory in order to develop a specific conception of institutional indoctrination: an educational institution indoctrinates when it exercises its authority in order to support the deliberative norm that some belief P ought to be exempt from tests of or challenges to its truth or rightness just because it is belief P. Martin argues that this norm undermines conditions of symmetrical and inclusive public discourse essential to the development of knowledge and understanding among free and equal citizens. That is, institutional indoctrination involves a closing of the public mind.
No evidence for the effect of entrainment's phase on duration reproduction and precision of regular intervals
Authors: Houshmand Chatroudi Amirmahmoud , Yotsumoto Yuko
Published: June 2023

Perception of time is not always veridical; rather, it is subjected to distortions. One such compelling distortion is that the duration of regularly spaced intervals is often overestimated. One account suggests that excitatory phases of neural entrainment concomitant with such stimuli play a major role. However, assessing the correlation between the power of entrained oscillations and time dilation has yielded inconclusive results. In this study, we evaluated whether phase characteristics of neural oscillations impact time dilation. For this purpose, we entrained 10‐Hz oscillations and experimentally manipulated the presentation of flickers so that they were presented either in‐phase or out‐of‐phase relative to the established rhythm. Simultaneous electroencephalography (EEG) recordings confirmed that in‐phase and out‐of‐phase flickers had landed on different inhibitory phases of high‐amplitude alpha oscillations. Moreover, to control for confounding factors of expectancy and masking, we created two additional conditions. Results, supplemented by the Bayesian analysis, indicated that the phase of entrained visual alpha oscillation does not differentially affect flicker‐induced time dilation. Repeating the same experiment with regularly spaced auditory stimuli replicated the null findings. Moreover, we found a robust enhancement of precision for the reproduction of flickers relative to static stimuli that were partially supported by entrainment models. We discussed our results within the framework of neural oscillations and time‐perception models, suggesting that inhibitory cycles of visual alpha may have little relevance to the overestimation of regularly spaced intervals. Moreover, based on our findings, we proposed that temporal oscillators, assumed in entrainment models, may act independently of excitatory phases in the brain's lower level sensory areas.
Defining Test‐Score Interpretation, Use, and Claims: Delphi Study for the Validity Argument
Authors: Folger Timothy D. , Bostic Jonathan , Krupa Erin E.
Published: June 2023

Validity is a fundamental consideration of test development and test evaluation. The purpose of this study is to define and reify three key aspects of validity and validation, namely test‐score interpretation, test‐score use, and the claims supporting interpretation and use. This study employed a Delphi methodology to explore how experts in validity and validation conceptualize test‐score interpretation, use, and claims. Definitions were developed through multiple iterations of data collection and analysis. By clarifying the language used when conducting validation, validation may be more accessible to a broader audience, including but not limited to test developers, test users, and test consumers.
Identification of novel mutations in patients with Diamond‐Blackfan anemia and literature review of RPS10 and RPS26 mutations
Authors: Li Jing , Su Yongfeng , Chen Long , Lin Yani , Ru Kun
Published: June 2023

Introduction

Diamond‐Blackfan anemia (DBA) is a rare congenital bone marrow failure syndrome characterized by erythroid aplasia, physical malformation, and cancer predisposition. Twenty ribosomal protein genes and three non‐ribosomal protein genes have been identified associated with DBA.

Methods

To investigate the presence of novel mutations and gain a deeper understanding of the molecular mechanisms of disease, targeted next‐generation sequencing was performed in 12 patients with clinically suspected DBA. Literatures were retrieved with complete clinical information published in English by November 2022. The clinical features, treatment, and RPS10/RPS26 mutations were analyzed.

Results

Among the 12 patients, 11 mutations were identified and 5 of them were novel (RPS19, p.W52S; RPS10, p.P106Qfs*11; RPS26, p.R28*; RPL5, p.R35*; RPL11, p.T44Lfs*40). Including 2 patients in this study, 13 patients with RPS10 mutations and 38 patients with RPS26 mutations were reported from 4 and 6 countries, respectively. The incidences of physical malformation in patients with RPS10 and RPS26 mutations (22% and 36%, respectively) were lower than the overall incidence in DBA patients (~50%). Patients with RPS26 mutations had a worse response rate of steroid therapy than RPS10 (47% vs. 87.5%), but preferred RBC transfusions (67% vs. 44%, p = 0.0253).

Conclusion

Our findings add to the DBA pathogenic variant database and demonstrate the clinical presentations of the DBA patients with RPS10/RPS26 mutations. It shows that next‐generation sequencing is a powerful tool for the diagnosis of genetic diseases such as DBA.
Changing pattern of respiratory virus detections among school‐aged children in a small community – Dane County, Wisconsin, September to December 2022
Authors: Temte Jonathan L. , Goss Maureen , Bell Cristalyne , Barlow Shari , Temte Emily , Bateman Allen , Uzicanin Amra
Published: June 2023

Widespread school closures and other non‐pharmaceutical interventions (NPIs), used to limit the spread of SARS‐CoV‐2, significantly disrupted transmission patterns of seasonal respiratory viruses. As NPIs were relaxed, populations were vulnerable to resurgence. This study within a small community assessed acute respiratory illness among kindergarten through grade 12 students as they returned to public schools from September through December 2022 without masking and distancing requirements. The 277 specimens collected demonstrated a shift from rhinovirus to influenza. With continued circulation of SARS‐CoV‐2 and return of seasonal respiratory viruses, understanding evolving transmission patterns will play an important role in reducing disease burden.
Chewing performance of patients with worn dentition before and after restorations: A scoping review
Authors: Carboncini Fabio , Landi Matteo , Rossit Marco , Saracutu Ovidiu Ionut , Ferrari Marco , Manfredini Daniele
Published: June 2023

Background

Tooth wear is a multifactorial complex process related to the loss of dental tissue, due to chemical or mechanical processes, by abrasion, attrition, erosion. Restorative treatment represents an attempt to rebuild and recreate the lost structure.

Objective

This scoping review aims to investigate whether restorative treatment of worn dentition (either with direct or indirect adhesive composite adhesive procedures or with prosthetic techniques) can have an impact on the masticatory performance parameters.

Methods

A scoping review was conducted on multiple databases (Pubmed, Medline CENTRAL, ICTRP), following the PRISMA guidelines. Abstracts of research papers were screened for suitability, and full‐text articles were obtained for those who satisfied the inclusion and exclusion criteria.

Results

Only one article meet the inclusion criteria of the review. Restorative treatment of worn dentition although have a positive impact on the self‐report ability to chew, has no effect on the masticatory performance test.

Conclusion

At the moment, not enough evidence to comment on the actual therapeutic role of restorative treatment on tooth wear is available. Clinicians, before taking any clinical decision, should carefully discuss with patients the needs and expectations of the treatment plan.
Octospy: What Octopus insularis do in their dens
Authors: O'Brien C. E. , Medeiros Sylvia Lima de Souza , Leite Tatiana
Published: June 2023

Octopus insularis is a benthic octopod from the tropical and subtropical Western Atlantic Ocean that inhabits semi‐permanent “dens” (small crevices) in hard substrate. We used visual surveys to assess den occupancy and remote cameras at den entrances to assess activity patterns of O. insularis of South Caicos (21.5112° N, 71.5190° W) in the Turks and Caicos Islands (May–August, 2020 and July–December, 2021). Dens were occupied for a median of 4 days, but occupancy ranged widely (1 day–2 months), indicating migration between dens at erratic intervals. The two most prevalent behaviors were Away from the Den, time presumably spent mostly foraging, and Quiescence, when the octopus was sleeping or otherwise unreactive. Our data indicate that Octopus insularis is diurnal, with time Away from the Den peaking between mid‐morning (0700–1000) and late afternoon (1600–2000), and with Quiescence peaking at night (2000–0600) and also in the middle of the day (1100–1600), although adherence to this pattern was not strict. High interindividual variation and high within‐individual stability in the proportions of time Away from the Den and Quiescent suggest that individuals of this species vary greatly from each other in their hunting and resting patterns, while also showing high levels of internal consistency for at least a week. These observations will guide future research with this commercially important species, further differentiates O. insularis from congeners, and demonstrate the efficacy of minimally disruptive field techniques in studying behavior.
The influence of soft contact lens material on the corneoscleral profile
Authors: Consejo Alejandra , Roll Vanesa , Roman Denisa M. , Remon Laura
Published: June 2023

Purpose

To objectively quantify changes in corneoscleral profile, as evaluated by the limbus position and corneoscleral junction (CSJ) angle, as a consequence of wearing different soft contact lens (CL) materials.

Methods

Twenty‐two healthy participants wore silicone hydrogel (SiHy, MyDay, CooperVision) and hydrogel (Hy, Biomedics 1 day extra, CooperVision) soft CLs for 8 h per lens in their left eye. In each session, corneoscleral topography was captured before and immediately after CL removal with an Eye Surface Profiler. Previously validated automatic and objective algorithms for limbal position and CSJ angle calculation were applied to 360 semi‐meridians to investigate the effect of short‐term CL wear on corneoscleral topography, globally and by sectors, depending on the soft CL material worn.

Results

Short‐term soft CL wear significantly impacted limbal position (SiHy: 120 ± 97 μm, Hy: 128 ± 85 μm) and CSJ angle (SiHy: 0.57 ± 0.36°, Hy: 0.55 ± 0.40°); all p < 0.05. A statistically significant difference was found between the sectors with regard to limbus position and CSJ angle before CL wear that remained following lens wear (all pairwise comparisons, p < 0.001). Although individual differences were observed, there was no evidence that one material caused more substantial corneoscleral alterations.

Conclusion

Corneoscleral profile parameters were altered significantly following 8 h of soft CL wear. The observed changes in limbus position and CSJ angle support the importance of participant‐material biocompatibility.
Axillary vein puncture versus cephalic vein cutdown for cardiac implantable electronic device implantation: A meta‐analysis
Authors: Vetta Giampaolo , Magnocavallo Michele , Parlavecchio Antonio , Caminiti Rodolfo , Polselli Marco , Sorgente Antonio , Cauti Filippo Maria , Crea Pasquale , Pannone Luigi , Marcon Lorenzo , Savio Armando Lo , Pistelli Lorenzo , Vetta Francesco , Chierchia Gian‐Battista , Rossi Pietro , Bianchi Stefano , Natale Andrea , de Asmundis Carlo , Rocca Domenico G. Della
Published: June 2023

Introduction

Cephalic vein cutdown (CVC) and axillary vein puncture (AVP) are both recommended for transvenous implantation of leads for cardiac implantable electronic devices (CIEDs). Nonetheless, it is still debated which of the two techniques has a better safety and efficacy profile.

Methods

We systematically searched Medline, Embase, and Cochrane electronic databases up to September 5, 2022, for studies that evaluated the efficacy and safety of AVP and CVC reporting at least one clinical outcome of interest. The primary endpoints were acute procedural success and overall complications. The effect size was estimated using a random‐effect model as risk ratio (RR) and relative 95% confidence interval (CI).

Results

Overall, seven studies were included, which enrolled 1771 and 3067 transvenous leads (65.6% [n = 1162] males, average age 73.4 ± 14.3 years). Compared to CVC, AVP showed a significant increase in the primary endpoint (95.7 % vs. 76.1 %; RR: 1.24; 95% CI: 1.09–1.40; p = .001) (Figure 1). Total procedural time (mean difference [MD]: −8.25 min; 95% CI: −10.23 to −6.27; p < .0001; I2 = 0%) and venous access time (MD: −6.24 min; 95% CI: −7.01 to −5.47; p < .0001; I2 = 0%) were significantly shorter with AVP compared to CVC. No differences were found between AVP and CVC for incidence overall complications (RR: 0.56; 95% CI: 0.28–1.10; p = .09), pneumothorax (RR: 0.72; 95% CI: 0.13−4.0; p = .71), lead failure (RR: 0.58; 95% CI: 0.23–1.48; p = .26), pocket hematoma/bleeding (RR: 0.58; 95% CI: 0.15–2.23; p = .43), device infection (RR: 0.95; 95% CI: 0.14–6.60; p = .96) and fluoroscopy time (MD: −0.24 min; 95% CI: −0.75 to 0.28; p = .36).

Conclusion

Our meta‐analysis suggests that AVP may improve procedural success and reduce total procedural time and venous access time compared to CVC.
Left atrial functions in the early period after cryoballoon ablation for paroxysmal atrial fibrillation
Authors: Soysal Ali Ugur , Ozturk Sila , Onder Sukriye Ebru , Atici Adem , Tokdil Hasan , Raimoglu Utku , Gulfidan Asli , Yalman Hakan , Durmaz Eser , Ikitimur Baris , Yalin Kivanc
Published: June 2023

Purpose

In patients with paroxysmal atrial fibrillation (PAF), functional changes are observed in the left atrium (LA) after pulmonary vein isolation (PVI) procedure. Although previous studies have investigated the altered mechanical functions of the LA with radiofrequency (RF) ablation, changes in the LA functions in the early period after cryoablation (CB‐2) have not been clearly demonstrated. This study aims to explore the early periodical changes in mechanical functions of the LA in patients with PAF who underwent CB‐2 based ablation through the help of echocardiographic methods which contain Doppler and strain parameters.

Methods

Consecutive 77 patients (mean age: 57.5 ±  11.2; 57% men) with PAF underwent CB‐2 were prospectively analyzed. All patients were in sinus rhythm before and after the procedure. The LA dimensions, the LA reservoir strain, the LA atrial contractile strain and the LA conduit strain and left ventricular diastolic function parameters were evaluated by Doppler echocardiography before and 3 months after the procedure.

Results

Acute procedural success was achieved in all cases. No major complications were observed. LA reservoir strain and LA contractile strain showed significant recovery after the procedure. (28.3 ± 12.8 vs. 34.6 ± 13.8, p < .001 and −10.8 ± 7.9 vs. −13.9 ± 9.3, p = .014 respectively). No significant change was demonstrated in other echocardiographic parameters.

Conclusion

Significant improvement in mechanical functions may occur even in the early period after cryoballoon ablation in patients with PAF.