bluuebunny/crossref_metadata_2025 huggingface dataset:
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors
Authors: Hoffmann Markus , Trummer Nico , Schwartz Leon , Jankowski Jakub , Lee Hye Kyung , Willruth Lina-Liv , Lazareva Olga , Yuan Kevin , Baumgarten Nina , Schmidt Florian , Baumbach Jan , Schulz Marcel H , Blumenthal David B , Hennighausen Lothar , List Markus
Published: May 2023

Background

Eukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound by transcription factors (TFs). Differential expression of TFs and their binding affinity at putative CREs determine tissue- and developmental-specific transcriptional activity. Consolidating genomic datasets can offer further insights into the accessibility of CREs, TF activity, and, thus, gene regulation. However, the integration and analysis of multimodal datasets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined chromatin state data (e.g., chromatin immunoprecipitation [ChIP], ATAC, or DNase sequencing) and RNA sequencing data exist, they do not offer convenient usability, have limited support for large-scale data processing, and provide only minimal functionality for visually interpreting results.

Results

We developed TF-Prioritizer, an automated pipeline that prioritizes condition-specific TFs from multimodal data and generates an interactive web report. We demonstrated its potential by identifying known TFs along with their target genes, as well as previously unreported TFs active in lactating mouse mammary glands. Additionally, we studied a variety of ENCODE datasets for cell lines K562 and MCF-7, including 12 histone modification ChIP sequencing as well as ATAC and DNase sequencing datasets, where we observe and discuss assay-specific differences.

Conclusion

TF-Prioritizer accepts ATAC, DNase, or ChIP sequencing and RNA sequencing data as input and identifies TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.
On the benefits of self-taught learning for brain decoding
Authors: Germani Elodie , Fromont Elisa , Maumet Camille
Published: May 2023

Context

We study the benefits of using a large public neuroimaging database composed of functional magnetic resonance imaging (fMRI) statistic maps, in a self-taught learning framework, for improving brain decoding on new tasks. First, we leverage the NeuroVault database to train, on a selection of relevant statistic maps, a convolutional autoencoder to reconstruct these maps. Then, we use this trained encoder to initialize a supervised convolutional neural network to classify tasks or cognitive processes of unseen statistic maps from large collections of the NeuroVault database.

Results

We show that such a self-taught learning process always improves the performance of the classifiers, but the magnitude of the benefits strongly depends on the number of samples available both for pretraining and fine-tuning the models and on the complexity of the targeted downstream task.

Conclusion

The pretrained model improves the classification performance and displays more generalizable features, less sensitive to individual differences.
3-D shallow shear velocity structure of the Jakarta Basin from transdimensional ambient noise tomography
Authors: Ry Rexha Verdhora , Cummins Phil R , Hejrani Babak , Widiyantoro Sri
Published: May 2023

Situated on the northern coast of the Indonesian island of Java, Jakarta and its metropolitan area (Greater Jakarta) are subject to significant earthquake hazards from a subduction zone south of Java and nearby active crustal faults. The seismic risk may be even higher because Greater Jakarta resides on a sedimentary basin filled with thick Pliocene–Pleistocene sediments. A comprehensive study of Jakarta Basin's properties and geometry is important for creating robust seismic hazard and risk assessments. The main objective of this study is to develop a 3-D model of Jakarta Basin's shallow shear-wave velocity (VS ) structure and improve on previous models that did not cover the basin edge due to the extent of data coverage. Between April and October 2018, we deployed a new temporary seismic network to extend the spatial coverage beyond that of a previous deployment in 2013, and sampled 143 locations through sequential deployments of 30 broad-band sensors covering Jakarta and its adjacent areas. We conducted a 2-stage transdimensional Bayesian inversion of Rayleigh wave phase velocity dispersion curves derived from seismic noise. To begin, we applied tomography and constructed 2-D phase velocity maps for periods 1–5 s. Then, at each point in a regular grid defined on these maps, we invert each dispersion curve into 1-D depth profiles of VS . Finally, these profiles at gridpoints with ∼2 km spacing are interpolated to form a pseudo-3-D VS model. Our results reveal the edge of the Pliocene–Pleistocene sediments along the south. Also, we resolve a basement offset across south Jakarta that we suggest may be related to the western extension of the Baribis Fault (alternatively, the West Java Backarc Thrust). We recommend using this 3-D model of the Jakarta Basin for scenario earthquake ground motion simulations. Such simulations would help establish how important it might be to re-assess seismic hazard and risk in Greater Jakarta so that basin resonance and amplification are considered.
Robust global mantle flow trajectories and their validation via dynamic topography histories
Authors: Taiwo A , Bunge H-P , Schuberth B S A , Colli L , Vilacis B
Published: May 2023

The ability to construct time-trajectories of mantle flow is crucial to move from studies of instantaneous to time-dependent earth models and to exploit geological constraints for mantle convection modelling. However mantle convection is chaotic and subject to the butterfly effect: the trajectories of two identical mantle convection models initialized with slightly different temperature fields diverge exponentially in time until they become uncorrelated. Because one may use seismic inferences about the mantle state as a starting or terminal condition to project mantle flow forward or backward in time, and because the seismic inference is invariably subject to uncertainties, this seemingly would rule out any construction of robust mantle flow trajectories. Here we build upon earlier work which showed that assimilation of the horizontal component of the surface velocity field from a known reference model allows one to overcome the butterfly effect and to construct robust mantle flow trajectories, regardless of the choice of the initial state perturbation. To this end, we use high resolution 3-D spherical mantle convection models in four end-member configurations: an isoviscous purely internally heated model, an isoviscous purely bottom heated model, a model with a radial increase in viscosity along with pure internal heating as well as a model that combines the effects of radial viscosity increase, internal and bottom heating. In order to capture the impact of seismic filtering, we perturb the initial temperature fields of these end-member models through either radial or horizontal smoothing of the temperature field or the application of the tomographic filter of seismic model S20RTS. We assess the quality of the constructed model trajectories via a number of statistical measures as well as comparisons of their dynamic topography histories. The latter is an essential step since mantle flow cannot be directly observed but has to be inferred via its surface manifestations. Importantly, linking mantle flow to surface observations yields patterns representable on a latitude–longitude grid similar to meteorological observables such as precipitation. This invites the application of meteorological quality metrics, such as the power ratio and Taylor diagram, to assess the quality of mantle flow trajectories. We introduce these metrics for the first time in the context of mantle convection and demonstrate their viability based on the compact manner in which they summarize model performance.
Predictors of digital technology-based mental health programs in young adults for mental health support
Authors: Perich Tania , Andriessen Karl
Published: May 2023

Technology-based platforms are widely used to deliver mental health support. The aim of this study was to explore factors associated with the use of technology-based mental health platforms by students who may be vulnerable to develop a mental health condition in an Australian psychology student sample. Participants were 1146 students (18–30 years) at an Australian university who completed a survey regarding their current mental health symptoms and lifetime use of technology-based platforms. The student’s country of birth, having a previous mental health diagnosis, having a family member with a mental illness and greater stress scores predicted any type of online/technology-use. Greater symptoms correlated with lower helpfulness of online mental health programs and websites. Apps were perceived as more helpful by those with a mental illness history and associated with higher stress scores. The use of any type of technology-based platform was high in the sample overall. Further research may clarify why mental health programs are less popular, and how these platforms may be utilised to support mental health outcomes.
Bi-allelic variants inASTLcause abnormal fertilization or oocyte maturation defects
Authors: Zeng Yang , Chen Biaobang , Sun Yiming , Yang Aijun , Wu Ling , Li Bin , Mu Jian , Zhang Zhihua , Wang Wenjing , Zhou Zhou , Dong Jie , Liu Ruyi , Luo Yuxi , Sun Xiaoxi , Sang Qing , Kuang Yanping , Wang Lei
Published: May 2023

Fertilization is a fundamental process of development, and the blocking mechanisms act at the zona pellucida (ZP) and plasma membrane of the egg to prevent any additional sperm from binding, permeating and fusing after fertilization. In clinical practice, some couples undergoing recurrent IVF failures that mature oocytes had abnormal fertilization for unknown reason. Ovastacin encoded by ASTL cleave the ZP protein ZP2 and play a key role in preventing polyspermy. Here, we identified bi-allelic variants in ASTL that are mainly characterized by fertilization problems in humans. All four independent affected individuals had bi-allelic frameshift variants or predicted damaging missense variants, which follow a Mendelian recessive inheritance pattern. The frameshift variants significantly decreased the quantity of ASTL protein in vitro. And all missense variants affected the enzymatic activity that cleaves ZP2 in mouse egg in vitro. Three knock-in female mice (corresponding to three missense variants in patients) all show subfertility due to low embryo developmental potential. This work presents strong evidence that pathogenic variants in ASTL cause female infertility and provides a new genetic marker for the diagnosis of fertilization problems.
Constitutional parasitism, camouflage, and pretense: Shaping citizenship through subterfuge
Authors: Ahmed Farrah
Published: May 2023

Constitutional rights or values are sometimes used by governments to disguise, mask, or misdirect attention from the true nature of their actions. Such strategies of subterfuge are, by their nature, difficult to identify and prove. This article responds to the challenge of identifying and proving subterfuge by demonstrating three types of strategies of subterfuge governments may deploy. To that end it uses a close study of three strategies deployed in the Indian government’s defense of a controversial citizenship law. The first strategy is the introduction and incubation of nationalist versions of constitutional values, exemplified by the Indian government as it planted an alternative nationalist vision of secularism in legal and public discourse about citizenship. The second strategy is the appropriation of constitutional rights to serve as camouflage to deflect criticism of the government’s true aims; the Indian government illustrated this strategy as it used religious freedom to camouflage its goal of removing “infiltrators.” The third strategy is the appropriation of human rights precedents for state action which in fact breaches human rights. The article demonstrates how we might prove, identify, and establish each of these strategies, when they are at work.
Transparency in Infectious Disease Research: Meta-research Survey of Specialty Journals
Authors: Zavalis Emmanuel A , Contopoulos-Ioannidis Despina G , Ioannidis John P A
Published: May 2023

Background

Infectious diseases carry large global burdens and have implications for society at large. Therefore, reproducible, transparent research is extremely important.

Methods

We evaluated transparency indicators (code and data sharing, registration, and conflict and funding disclosures) in the 5340 PubMed Central Open Access articles published in 2019 or 2021 in the 9 most cited specialty journals in infectious diseases using the text-mining R package, rtransparent.

Results

A total of 5340 articles were evaluated (1860 published in 2019 and 3480 in 2021 [of which 1828 were on coronavirus disease 2019, or COVID-19]). Text mining identified code sharing in 98 (2%) articles, data sharing in 498 (9%), registration in 446 (8%), conflict of interest disclosures in 4209 (79%), and funding disclosures in 4866 (91%). There were substantial differences across the 9 journals: 1%–9% for code sharing, 5%–25% for data sharing, 1%–31% for registration, 7%–100% for conflicts of interest, and 65%–100% for funding disclosures. Validation-corrected imputed estimates were 3%, 11%, 8%, 79%, and 92%, respectively. There were no major differences between articles published in 2019 and non-COVID-19 articles in 2021. In 2021, non-COVID-19 articles had more data sharing (12%) than COVID-19 articles (4%).

Conclusions

Data sharing, code sharing, and registration are very uncommon in infectious disease specialty journals. Increased transparency is required.
Analysis of MDR in the predominant Streptococcus pneumoniae serotypes in Canada: the SAVE study, 2011–2020
Authors: Adam Heather J , Karlowsky James A , Baxter Melanie R , Schellenberg John , Golden Alyssa R , Martin Irene , Demczuk Walter , Mulvey Michael R , Zhanel George G
Published: May 2023

Objectives

To investigate the levels of MDR in the predominant serotypes of invasive Streptococcus pneumoniae isolated in Canada over a 10 year period.

Methods

All isolates were serotyped and had antimicrobial susceptibility testing performed, in accordance with CLSI guidelines (M07-11 Ed., 2018). Complete susceptibility profiles were available for 13 712 isolates. MDR was defined as resistance to three or more classes of antimicrobial agents (penicillin MIC ≥2 mg/L defined as resistant). Serotypes were determined by Quellung reaction.

Results

In total, 14 138 invasive isolates of S. pneumoniae were tested in the SAVE study (S. pneumoniae Serotyping and Antimicrobial Susceptibility: Assessment for Vaccine Efficacy in Canada), a collaboration between the Canadian Antimicrobial Resistance Alliance and Public Health Agency of Canada—National Microbiology Laboratory. The rate of MDR S. pneumoniae in SAVE was 6.6% (902/13 712). Annual rates of MDR S. pneumoniae decreased between 2011 and 2015 (8.5% to 5.7%) and increased between 2016 and 2020 (3.9% to 9.4%). Serotypes 19A and 15A were the most common serotypes demonstrating MDR (25.4% and 23.5% of the MDR isolates, respectively); however, the serotype diversity index increased from 0.7 in 2011 to 0.9 in 2020 with a statistically significant linear increasing trend (P < 0.001). In 2020, MDR isolates were frequently serotypes 4 and 12F in addition to serotypes 15A and 19A. In 2020, 27.3%, 45.5%, 50.5%, 65.7% and 68.7% of invasive MDR S. pneumoniae were serotypes included in the PCV10, PCV13, PCV15, PCV20 and PPSV23 vaccines, respectively.

Conclusions

Although current vaccine coverage of MDR S. pneumoniae in Canada is high, the increasing diversity of serotypes observed among the MDR isolates highlights the ability of S. pneumoniae to rapidly evolve.
Genomic investigation of the most common Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011–2020
Authors: Golden Alyssa R , Adam Heather J , Karlowsky James A , Baxter Melanie , Schellenberg John , Martin Irene , Demczuk Walter , Minion Jessica , Van Caeseele Paul , Kus Julianne V , McGeer Allison , Lefebvre Brigitte , Smadi Hanan , Haldane David , Yu Yang , Mead Kristen , Mulvey Michael R , Zhanel George G
Published: May 2023

Objectives

To investigate the lineages and genomic antimicrobial resistance (AMR) determinants of the 10 most common pneumococcal serotypes identified in Canada during the five most recent years of the SAVE study, in the context of the 10-year post-PCV13 period in Canada.

Methods

The 10 most common invasive Streptococcus pneumoniae serotypes collected by the SAVE study from 2016 to 2020 were 3, 22F, 9N, 8, 4, 12F, 19A, 33F, 23A and 15A. A random sample comprising ∼5% of each of these serotypes collected during each year of the full SAVE study (2011–2020) were selected for whole-genome sequencing (WGS) using the Illumina NextSeq platform. Phylogenomic analysis was performed using the SNVPhyl pipeline. WGS data were used to identify virulence genes of interest, sequence types, global pneumococcal sequence clusters (GPSC) and AMR determinants.

Results

Of the 10 serotypes analysed in this study, six increased significantly in prevalence from 2011 to 2020: 3, 4, 8, 9N, 23A and 33F (P ≤ 0.0201). Serotypes 12F and 15A remained stable in prevalence over time, while serotype 19A decreased in prevalence (P < 0.0001). The investigated serotypes represented four of the most prevalent international lineages causing non-vaccine serotype pneumococcal disease in the PCV13 era: GPSC3 (serotypes 8/33F), GPSC19 (22F), GPSC5 (23A) and GPSC26 (12F). Of these lineages, GPSC5 isolates were found to consistently possess the most AMR determinants. Commonly collected vaccine serotypes 3 and 4 were associated with GPSC12 and GPSC27, respectively. However, a more recently collected lineage of serotype 4 (GPSC192) was highly clonal and possessed AMR determinants.

Conclusions

Continued genomic surveillance of S. pneumoniae in Canada is essential to monitor for the appearance of new and evolving lineages, including antimicrobial-resistant GPSC5 and GPSC162.
Comparison of PCV10, PCV13, PCV15, PCV20 and PPSV23 vaccine coverage of invasive Streptococcus pneumoniae isolate serotypes in Canada: the SAVE study, 2011–20
Authors: Schellenberg John J , Adam Heather J , Baxter Melanie R , Karlowsky James A , Golden Alyssa R , Martin Irene , Demczuk Walter , Mulvey Michael R , Zhanel George G
Published: May 2023

Background

As pneumococci evolve under vaccine, antimicrobial and other selective pressures, it is important to track isolates covered by established (PCV10, PCV13 and PPSV23) and new (PCV15 and PCV20) vaccine formulations.

Objectives

To compare invasive pneumococcal disease (IPD) isolates from serotypes covered by PCV10, PCV13, PCV15, PCV20 and PPSV23, collected in Canada from 2011 to 2020, by demographic category and antimicrobial resistance phenotype.

Methods

IPD isolates from the SAVE study were initially collected by members of the Canadian Public Health Laboratory Network (CPHLN) as part of a collaboration between the Canadian Antimicrobial Resistance Alliance (CARA) and the Public Health Agency of Canada (PHAC). Serotypes were determined by quellung reaction, and antimicrobial susceptibility testing was performed using the CLSI broth microdilution method.

Results

A total of 14 138 invasive isolates were collected from 2011 to 2020, with 30.7% of isolates covered by the PCV13 vaccine, 43.6% of isolates covered by the PCV15 vaccine (including 12.9% non-PCV13 serotypes 22F and 33F), and 62.6% of isolates covered by the PCV20 vaccine (including 19.0% non-PCV15 serotypes 8, 10A, 11A, 12F and 15B/C). Non-PCV20 serotypes 2, 9N, 17F and 20, but not 6A (present in PPSV23) represented 8.8% of all IPD isolates. Higher-valency vaccine formulations covered significantly more isolates by age, sex, region and resistance phenotype including MDR isolates. Coverage of XDR isolates did not significantly differ between vaccine formulations.

Conclusions

When compared with PCV13 and PCV15, PCV20 covered significantly more IPD isolates stratified by patient age, region, sex, individual antimicrobial resistance phenotypes and MDR phenotype.
A survey of Salmonella, Escherichia coli, and antimicrobial resistance in frozen, part-cooked, breaded, or battered chicken products on retail sale in the UK
Authors: Willis Caroline , Jørgensen Frieda , Cawthraw Shaun , Aird Heather , Lai Sandra , Kesby Michelle , Chattaway Marie , Lock Ioana , Quill Emiline , Raykova Gabriela
Published: May 2023

Aim

Frozen, breaded chicken products have been implicated in Salmonella outbreaks, and may be incorrectly perceived as ready-to-eat, leading to mishandling or undercooking by consumers. This study aimed to assess the prevalence of Salmonella and antimicrobial resistant (AMR) Escherichia coli in these products.

Methods and results

Samples of frozen, raw, or partly cooked, coated chicken products were collected between April and July 2021 from retailers in the UK and tested for Salmonella spp., generic E. coli, extended spectrum beta-lactamase-producing, colistin-resistant, and carbapenem-resistant E. coli. One isolate of each bacterial type from each sample was selected for minimum inhibitory concentration determination for a range of antimicrobials. Salmonella was detected in 5 of 310 (1.6%) samples, identified as Salmonella Infantis in three samples and Salm. Java in two. One Salm. Infantis isolate was multidrug resistant, while the other Salmonella isolates were each resistant to at least one class of antimicrobials. Generic E. coli were detected in 113 samples (36.4%), with multidrug resistance being demonstrated in 20.0% of these. Escherichia coli with the ESBL phenotype were detected in 15 (4.8%) of samples and the AmpC phenotype in 2 (0.6%). A colistin-resistant E. coli was isolated from one sample; this possessed the mcr-1 gene. No carbapenem-resistant E. coli were detected. The five Salmonella-positive samples from this study, together with 20 Salmonella-positive products from an earlier study in 2020/2021, were cooked according to the manufacturers’ instructions. Following cooking, Salmonella was not detected in any samples.

Conclusions

This survey demonstrates continued contamination of frozen, coated chicken products with Salmonella, and provides data on the prevalence of AMR in these products.
The role of epithelial cells in the immunopathogenesis of Sjögren's syndrome
Authors: Tang Yuan , Zhou Yingbo , Wang Xiaoran , Che Nan , Tian Jie , Man Kwan , Rui Ke , Peng Na , Lu Liwei
Published: May 2023

Sjögren's syndrome is a systemic autoimmune disease characterized by dysfunction of the affected exocrine glands. Lymphocytic infiltration within the inflamed glands and aberrant B-cell hyperactivation are the two salient pathologic features in Sjögren's syndrome. Increasing evidence indicates that salivary gland epithelial cells act as a key regulator in the pathogenesis of Sjögren's syndrome, as revealed by the dysregulated innate immune signaling pathways in salivary gland epithelium and increased expression of various proinflammatory molecules as well as their interaction with immune cells. In addition, salivary gland epithelial cells can regulate adaptive immune responses as nonprofessional antigen-presenting cells and promote the activation and differentiation of infiltrated immune cells. Moreover, the local inflammatory milieu can modulate the survival of salivary gland epithelial cells, leading to enhanced apoptosis and pyroptosis with the release of intracellular autoantigens, which further contributes to SG autoimmune inflammation and tissue destruction in Sjögren's syndrome. Herein, we reviewed recent advances in elucidating the role of salivary gland epithelial cells in the pathogenesis of Sjögren's syndrome, which may provide rationales for potential therapeutic targeting of salivary gland epithelial cells to alleviate salivary gland dysfunction alongside treatments with immunosuppressive reagents in Sjögren's syndrome.
Death as the Cessation of an Organism and the Moral Status Alternative
Authors: Nowak Piotr Grzegorz
Published: May 2023

The mainstream concept of death—the biological one—identifies death with the cessation of an organism. In this article, I challenge the mainstream position, showing that there is no single well-established concept of an organism and no universal concept of death in biological terms. Moreover, some of the biological views on death, if applied in the context of bedside decisions, might imply unacceptable consequences. I argue the moral concept of death—one similar to that of Robert Veatch—overcomes such difficulties. The moral view identifies death with the irreversible cessation of a patient’s moral status, that is, a state when she can no longer be harmed or wronged. The death of a patient takes place when she is no longer capable of regaining her consciousness. In this regard, the proposal elaborated herein resembles that of Veatch yet differs from Veatch’s original project since it is universal. In essence, it is applicable in the case of other living beings such as animals and plants, provided that they have some moral status.
Evidence-based Medicine and Mechanistic Evidence: The Case of the Failed Rollout of Efavirenz in Zimbabwe
Authors: Park Andrew , Steel Daniel , Maine Elicia
Published: May 2023

Evidence-based medicine (EBM) has long deemphasized mechanistic reasoning and pathophysiological rationale in assessing the effectiveness of interventions. The EBM+ movement has challenged this stance, arguing that evidence of mechanisms and comparative studies should both be seen as necessary and complementary. Advocates of EBM+ provide a combination of theoretical arguments and examples of mechanistic reasoning in medical research. However, EBM+ proponents have not provided recent examples of how downplaying mechanistic reasoning resulted in worse medical results than would have occurred otherwise. Such examples are necessary to make the case that EBM+ responds to a problem in clinical practice that urgently demands a solution. In light of this, we examine the failed rollout of efavirenz as a first-line HIV treatment in Zimbabwe as evidence of the importance of mechanistic reasoning in improving clinical practice and public health policy decisions. We suggest that this case is analogous to examples commonly given to support EBM.
Analysis of person-hours required for proton beam therapy for pediatric tumors
Authors: Mizumoto Masashi , Fukushima Hiroko , Miyamoto Toshio , Oshiro Yoshiko , Sumiya Taisuke , Iizumi Takashi , Saito Takashi , Makishima Hirokazu , Numajiri Haruko , Hosaka Sho , Nagatomo Kumie , Yamaki Yuni , Nakai Kei , Sakurai Hideyuki
Published: May 2023

Proton beam therapy (PBT) is effective for pediatric tumors, but patients may require sedation and other preparations, which extend the treatment time. Pediatric patients were classified into sedation and non-sedation cases. Adult patients were classified into three groups based on irradiation from two directions without or with respiratory synchronization and patch irradiation. Treatment person-hours were calculated as follows: (time from entering to leaving the treatment room) × (number of required personnel). A detailed analysis showed that the person-hours required for the treatment of pediatric patients are about 1.4–3.5 times greater than those required for adult patients. With the inclusion of additional time for the preparation of pediatric patients, PBT for pediatric cases is two to four times more labor-intensive than for typical adult cases.
Negligible risk of surface transmission of SARS-CoV-2 in public transportation
Authors: Pilipenco Alina , Forinová Michala , Mašková Hana , Hönig Václav , Palus Martin , Lynn Jr. Nicholas Scott , Víšová Ivana , Vrabcová Markéta , Houska Milan , Anthi Judita , Spasovová Monika , Mustacová Johana , Štěrba Ján , Dostálek Jakub , Tung Chao-Ping , Yang An-Suei , Jack Rachael , Dejneka Alexandr , Hajdu Janos , Vaisocherová-Lísalová Hana
Published: May 2023

Background

Exposure to pathogens in public transport systems is a common means of spreading infection, mainly by inhaling aerosol or droplets from infected individuals. Such particles also contaminate surfaces, creating a potential surface-transmission pathway.

Methods

A fast acoustic biosensor with an antifouling nano-coating was introduced to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on exposed surfaces in the Prague Public Transport System. Samples were measured directly without pre-treatment. Results with the sensor gave excellent agreement with parallel quantitative reverse-transcription polymerase chain reaction (qRT-PCR) measurements on 482 surface samples taken from actively used trams, buses, metro trains and platforms between 7 and 9 April 2021, in the middle of the lineage Alpha SARS-CoV-2 epidemic wave when 1 in 240 people were COVID-19 positive in Prague.

Results

Only ten of the 482 surface swabs produced positive results and none of them contained virus particles capable of replication, indicating that positive samples contained inactive virus particles and/or fragments. Measurements of the rate of decay of SARS-CoV-2 on frequently touched surface materials showed that the virus did not remain viable longer than 1–4 h. The rate of inactivation was the fastest on rubber handrails in metro escalators and the slowest on hard-plastic seats, window glasses and stainless-steel grab rails. As a result of this study, Prague Public Transport Systems revised their cleaning protocols and the lengths of parking times during the pandemic.

Conclusions

Our findings suggest that surface transmission played no or negligible role in spreading SARS-CoV-2 in Prague. The results also demonstrate the potential of the new biosensor to serve as a complementary screening tool in epidemic monitoring and prognosis.
Tacit Concepts of Family in Legislation on Assisted Reproduction
Authors: Pedersen Frank H
Published: May 2023

This article examines the joint corpus of family and health legislation and practices to analyse the notions behind the Danish regulation of assisted reproduction. It introduces an analytical framework, which encompasses a more comprehensive approach and encapsulates the variety of regulatory tools that expressly or implicitly create restrictions on the provision of assisted reproduction. By providing a generally applicable framework for analyses of the de facto regulation to expose possible underlying tacit concepts, this article makes a methodological contribution to enhance the understanding of the intermingling fields of family and reproductive law. The analysis in this article shows that eligibility for receiving infertility care depends on one’s current family constellation and it is not children per se, which are the focal point. Surprisingly neither is the nuclear family. Rather, the consummation of the relationship between a man and a woman through one shared child is at the core of the regulation. Archaic notions of family and gender expectations are thus revealed. The article concludes by discussing how the raison d'être behind the regulation could have been something other than a specific concept of family. In this way, the article invites others to analyse their national regulation of assisted reproduction and to contribute to an international discussion about whom, in the pursuit of family formation through ART treatment, has an underprivileged status.
The bright extragalactic ALMA redshift survey (BEARS) – II. Millimetre photometry of gravitational lens candidates
Authors: Bendo G J , Urquhart S A , Serjeant S , Bakx T , Hagimoto M , Cox P , Neri R , Lehnert M D , Dannerbauer H , Amvrosiadis A , Andreani P , Baker A J , Beelen A , Berta S , Borsato E , Buat V , Butler K M , Cooray A , De Zotti G , Dunne L , Dye S , Eales S , Enia A , Fan L , Gavazzi R , González-Nuevo J , Harris A I , Herrera C N , Hughes D H , Ismail D , Jones B M , Kohno K , Krips M , Lagache G , Marchetti L , Massardi M , Messias H , Negrello M , Omont A , Pérez-Fournon I , Riechers D A , Scott D , Smith M W L , Stanley F , Tamura Y , Temi P , van der Werf P , Verma A , Vlahakis C , Weiß A , Yang C , Young A J
Published: May 2023

We present 101- and 151-GHz ALMA continuum images for 85 fields selected from Herschel observations that have 500-μm flux densities >80 mJy and 250–500-μm colours consistent with z > 2, most of which are expected to be gravitationally lensed or hyperluminous infrared galaxies. Approximately half of the Herschel 500-μm sources were resolved into multiple ALMA sources, but 11 of the 15 brightest 500-μm Herschel sources correspond to individual ALMA sources. For the 37 fields containing either a single source with a spectroscopic redshift or two sources with the same spectroscopic redshift, we examined the colour temperatures and dust emissivity indices. The colour temperatures only vary weakly with redshift and are statistically consistent with no redshift-dependent temperature variations, which generally corresponds to results from other samples selected in far-infrared, submillimetre, or millimetre bands but not to results from samples selected in optical or near-infrared bands. The dust emissivity indices, with very few exceptions, are largely consistent with a value of 2. We also compared spectroscopic redshifts to photometric redshifts based on spectral energy distribution templates designed for infrared-bright high-redshift galaxies. While the templates systematically underestimate the redshifts by ∼15 per cent, the inclusion of ALMA data decreases the scatter in the predicted redshifts by a factor of ∼2, illustrating the potential usefulness of these millimetre data for estimating photometric redshifts.
WISDOM project – XIV. SMBH mass in the early-type galaxies NGC 0612, NGC 1574, and NGC 4261 from CO dynamical modelling
Authors: Ruffa Ilaria , Davis Timothy A , Cappellari Michele , Bureau Martin , Elford Jacob , Iguchi Satoru , Lelli Federico , Liang Fu-Heng , Liu Lijie , Lu Anan , Sarzi Marc , Williams Thomas G
Published: May 2023

We present a CO dynamical estimate of the mass of the supermassive black hole (SMBH) in three nearby early-type galaxies: NGC 0612, NGC 1574, and NGC 4261. Our analysis is based on Atacama Large Millimeter/submillimeter Array (ALMA) Cycle 3–6 observations of the 12CO(2–1) emission line with spatial resolutions of 14–58 pc (0.01″–0.26″). We detect disc-like CO distributions on scales from ≲ 200 pc (NGC 1574 and NGC 4261) to ≈10 kpc (NGC 0612). In NGC 0612 and NGC 1574 the bulk of the gas is regularly rotating. The data also provide evidence for the presence of a massive dark object at the centre of NGC 1574, allowing us to obtain the first measure of its mass, MBH = (1.0 ± 0.2) × 108 M⊙ (1σ uncertainty). In NGC 4261, the CO kinematics is clearly dominated by the SMBH gravitational influence, allowing us to determine an accurate black hole mass of (1.62 ± 0.04) × 109 M⊙ (1σ uncertainty). This is fully consistent with a previous CO dynamical estimate obtained using a different modelling technique. Signs of non-circular gas motions (likely outflow) are also identified in the inner regions of NGC 4261. In NGC 0612, we are only able to obtain a (conservative) upper limit of MBH ≲ 3.2 × 109 M⊙. This has likely to be ascribed to the presence of a central CO hole (with a radius much larger than that of the SMBH sphere of influence), combined with the inability of obtaining a robust prediction for the CO velocity curve. The three SMBH mass estimates are overall in agreement with predictions from the MBH − σ* relation.
Numerical discreteness errors in multispecies cosmological N-body simulations
Authors: Liu Xin , Emberson J D , Buehlmann Michael , Frontiere Nicholas , Habib Salman
Published: May 2023

We present a detailed analysis of numerical discreteness errors in two-species, gravity-only, cosmological simulations using the density power spectrum as a diagnostic probe. In a simple set-up where both species are initialized with the same total matter transfer function, biased growth of power forms on small scales when the solver force resolution is finer than the mean interparticle separation. The artificial bias is more severe when individual density and velocity transfer functions are applied. In particular, significant large-scale offsets in power are measured between simulations with conventional offset grid initial conditions when compared against converged high-resolution results where the force resolution scale is matched to the interparticle separation. These offsets persist even when the cosmology is chosen so that the two particle species have the same mass, indicating that the error is sourced from discreteness in the total matter field as opposed to unequal particle mass. We further investigate two mitigation strategies to address discreteness errors: the frozen potential method and softened interspecies short-range forces. The former evolves particles under the approximately ‘frozen’ total matter potential in linear theory at early times, while the latter filters cross-species gravitational interactions on small scales in low-density regions. By modelling closer to the continuum limit, both mitigation strategies demonstrate considerable reductions in large-scale power spectrum offsets.
Surface magnetism in the pulsating RV Tauri star R Scuti
Authors: Georgiev Stefan , Lèbre Agnès , Josselin Eric , Mathias Philippe , Konstantinova-Antova Renada , Sabin Laurence
Published: May 2023

We present the surface magnetic field conditions of the brightest pulsating RV Tauri star, R Sct. Our investigation is based on the longest spectropolarimetric survey ever performed on this variable star. The analysis of high resolution spectra and circular polarization data give sharp information on the dynamics of the atmosphere and the surface magnetism, respectively. Our analysis shows that surface magnetic field can be detected at different phases along a pulsating cycle, and that it may be related to the presence of a radiative shock wave periodically emerging out of the photosphere and propagating throughout the stellar atmosphere.
WISDOM Project – XV. Giant molecular clouds in the central region of the barred spiral galaxy NGC 5806
Authors: Choi Woorak , Liu Lijie , Bureau Martin , Cappellari Michele , Davis Timothy A , Gensior Jindra , Liang Fu-Heng , Lu Anan , Williams Thomas G , Chung Aeree
Published: May 2023

We present high spatial resolution (≈24 pc) Atacama Large Millimeter/sub-millimeter Array 12CO(2-1) observations of the central region of the nearby barred spiral galaxy NGC 5806. NGC 5806 has a highly structured molecular gas distribution with a clear nucleus, a nuclear ring, and offset dust lanes. We identify 170 spatially and spectrally resolved giant molecular clouds (GMCs). These clouds have comparable sizes (Rc) and larger gas masses, observed linewidths (σobs, los), and gas mass surface densities than those of clouds in the Milky Way disc. The size–linewidth relation of the clouds is one of the steepest reported so far ($\sigma _{\mathrm{obs,los}}\propto R_{\mathrm{c}}^{1.20}$ ), the clouds are on average only marginally bound (with a mean virial parameter 〈αvir〉 ≈ 2), and high velocity dispersions are observed in the nuclear ring. These behaviours are likely due to bar-driven gas shocks and inflows along the offset dust lanes, and we infer an inflow velocity of ≈120 km s−1 and a total molecular gas mass inflow rate of ≈5 M⊙ yr−1 into the nuclear ring. The observed internal velocity gradients of the clouds are consistent with internal turbulence. The number of clouds in the nuclear ring decreases with azimuthal angle downstream from the dust lanes without clear variation of cloud properties. This is likely due to the estimated short lifetime of the clouds (≈6 Myr), which appears to be mainly regulated by cloud–cloud collision and/or shear processes. Overall, it thus seems that the presence of the large-scale bar and gas inflows to the centre of NGC 5806 affect cloud properties.
Sensitivity of non-radiative cloud–wind interactions to the hydrodynamic solver
Authors: Braspenning Joey , Schaye Joop , Borrow Josh , Schaller Matthieu
Published: May 2023

Cloud–wind interactions are common in the interstellar and circumgalactic media. Many studies have used simulations of such interactions to investigate the effect of particular physical processes, but the impact of the choice of hydrodynamic solver has largely been overlooked. Here we study the cloud–wind interaction, also known as the ‘blob test’, using seven different hydrodynamic solvers: three flavours of SPH, a moving mesh, adaptive mesh refinement, and two meshless schemes. The evolution of masses in dense gas and intermediate-temperature gas, as well as the covering fraction of intermediate-temperature gas, are systematically compared for initial density contrasts of 10 and 100, and five numerical resolutions. To isolate the differences due to the hydrodynamic solvers, we use idealized non-radiative simulations without physical conduction. We find large differences between these methods. SPH methods show slower dispersal of the cloud, particularly for the higher density contrast, but faster convergence, especially for the lower density contrast. Predictions for the intermediate-temperature gas differ particularly strongly, also between non-SPH codes, and converge most slowly. We conclude that the hydrodynamical interaction between a dense cloud and a supersonic wind remains an unsolved problem. Studies aiming to understand the physics or observational signatures of cloud–wind interactions should test the robustness of their results by comparing different hydrodynamic solvers.
Biases to primordial non-Gaussianity measurements from CMB secondary anisotropies
Authors: Coulton William , Miranthis Alexander , Challinor Anthony
Published: May 2023

Our view of the last-scattering surface in the cosmic microwave background (CMB) is obscured by secondary anisotropies, sourced by scattering, extragalactic emission, and gravitational processes between recombination and observation. Whilst it is established that non-Gaussianity from the correlation between the integrated-Sachs–Wolfe (ISW) effect and gravitational lensing can significantly bias primordial non-Gaussianity (PNG) searches, recent work by Hill suggests that other combinations of secondary anisotropies can also produce significant biases. Building on that work, we use the WebSky and Sehgal et al. simulations to perform an extensive examination of possible biases to PNG measurements for the local, equilateral and orthogonal shapes. For a Planck-like CMB experiment, without foreground cleaning, we find significant biases from cosmic infrared background (CIB)-lensing and thermal Sunyaev–Zel’dovich (tSZ)-lensing bispectra for the local and orthogonal templates, and from CIB and tSZ bispectra for the equilateral template. For future experiments, such as the Simons Observatory, biases from correlations between the ISW effect and the tSZ and CIB will also become important. Finally, we investigate the effectiveness of foreground-cleaning techniques to suppress these biases. We find that the majority of these biases are effectively suppressed by the internal-linear combination method with a total bias below the $1\, \sigma$ statistical error for both experiments. However, the small total bias arises from the cancellation of several $1\, \sigma$ biases for Planck-like experiments and $2\, \sigma$ biases for SO-like. As this cancellation is likely sensitive to the modelling, to ensure robustness against these biases, we recommend that explicit removal methods should be used.
Thermal evolution of neutron stars in soft X-ray transients with thermodynamically consistent models of the accreted crust
Authors: Potekhin A Y , Gusakov M E , Chugunov A I
Published: May 2023

Thermal emission of neutron stars in soft X-ray transients (SXTs) in a quiescent state is believed to be powered by the heat deposited in the stellar crust due to nuclear reactions during accretion (deep crustal heating paradigm). Confronting observations of SXTs with simulations helps to verify theoretical models of the dense matter in the neutron stars. Usually, such simulations were carried out assuming that the free neutrons and nuclei in the inner crust move together. A recently proposed thermodynamically consistent approach allows for independent motion of the free neutrons. We simulate the thermal evolution of the SXTs within the thermodynamically consistent approach and compare the results with the traditional approach and with observations. For the latter, we consider a collection of quasi-equilibrium thermal luminosities of the SXTs in quiescence and the observed neutron star crust cooling in SXT MXB 1659−29. We test different models of the equation of state and baryon superfluidity and take into account additional heat sources in the shallow layers of neutron-star crust (the shallow heating). We find that the observed quasi-stationary thermal luminosities of the SXTs can be equally well fitted using the traditional and thermodynamically consistent models, provided that the shallow heat diffusion into the core is taken into account. The observed crust cooling in MXB 1659−29 can also be fitted in the frames of both models, but the choice of the model affects the derived parameters responsible for the thermal conductivity in the crust and for the shallow heating.
An XMM–Newton study of six narrow-line Seyfert 1 galaxies at z = 0.35–0.92
Authors: Yu Zhibo , Jiang Jiachen , Bambi Cosimo , Gallo Luigi C , Grupe Dirk , Fabian Andrew C , Reynolds Christopher S , Brandt William N
Published: May 2023

We report a detailed analysis of the XMM–Newton spectra of six narrow-line Seyfert 1 (NLS1) galaxies at redshift z  = 0.35–0.92. Compared with the NLS1s at lower redshift in the previously most-studied sample, these NLS1s have larger black hole (BH) masses ($\log \, M_\mathrm{BH}\gt 7.5$ ) with similar or even lower Eddington ratios. Our extended XMM–Newton sample of NLS1s shows strong soft X-ray excess emission below 2 keV. The quantified soft excess strength does not show an obvious discrepancy from previous studies of the lower redshift NLS1s. The systematic effect in the measurement of the Eddington ratio mainly lies in the bolometric correction factor. We also tentatively fit the spectra assuming two more physical models for the soft excess: warm Comptonization and relativistic reflection from the inner accretion disc. In the first scenario, we confirm the ubiquity of a warm and optically thick corona. The behaviour of a single source can be better explained by relativistic reflection, although we cannot distinguish which model is a more favourable explanation for the soft excess based on the best-fitting statistics.