bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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 &lt; 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

Abstract

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 &lt; 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

Abstract

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

Abstract

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

Abstract
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

AbstractThe 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

Abstract
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

Abstract
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

Abstract

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

Abstract
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

ABSTRACT
We present 101- and 151-GHz ALMA continuum images for 85 fields selected from Herschel observations that have 500-μm flux densities &gt;80 mJy and 250–500-μm colours consistent with z &gt; 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

ABSTRACT
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

ABSTRACT
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.