bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core and auxiliary functions of one-carbon metabolism in
Pseudomonas putida
exposed by a systems-level analysis of transcriptional and physiological responses
Authors: Turlin Justine , Puiggené Òscar , Donati Stefano , Wirth Nicolas T. , Nikel Pablo I. 
Published: June 2023

ABSTRACT

The soil bacterium
Pseudomonas putida
is a robust biomanufacturing host that assimilates a broad range of substrates while efficiently coping with adverse environmental conditions.
P. putida
is equipped with functions related to one-carbon (C1) compounds (e.g. methanol, formaldehyde, and formate) oxidation—yet pathways to assimilate these carbon sources are largely absent. In this work, we adopted a systems-level approach to study the genetic and molecular basis of C1 metabolism in
P. putida
. RNA sequencing identified two oxidoreductases, encoded by
PP_0256
and
PP_4596
, transcriptionally active in the presence of formate. Quantitative physiology of deletion mutants revealed growth defects at high formate concentrations, pointing to an important role of these oxidoreductases in C1 tolerance. Moreover, we describe a concerted detoxification process for methanol and formaldehyde, the C1 intermediates upstream formate. Alcohol oxidation to highly-reactive formaldehyde by PedEH and other broad-substrate-range dehydrogenases underpinned the (apparent) suboptimal methanol tolerance of
P. putida
. Formaldehyde was mostly processed by a glutathione-dependent mechanism encoded in the
frmAC
operon, and thiol-independent FdhAB and AldB-II overtook detoxification at high aldehyde concentrations. Deletion strains were constructed and characterized towards unveiling these biochemical mechanisms, underscoring the worth of
P. putida
for emergent biotechnological applications—e.g. engineering synthetic formatotrophy and methylotrophy.

IMPORTANCE

C1 substrates continue to attract interest in biotechnology, as their use is both cost-effective and ultimately expected to mitigate the impact of greenhouse gas emissions. However, our current understanding of bacterial C1 metabolism remains relatively limited in species that cannot grow on (i.e., assimilate) these substrates.
Pseudomonas putida
, a model Gram-negative environmental bacterium, constitutes a prime example of this sort. The biochemical pathways active in response to methanol, formaldehyde, and formate have been largely overlooked—although the ability of
P. putida
to process C1 molecules has been previously alluded to in the literature. By using a systems-level strategy, this study bridges such knowledge gap through the identification and characterization of mechanisms underlying methanol, formaldehyde, and formate detoxification—including hitherto unknown enzymes that act on these substrates. The results reported herein both expand our understanding of microbial metabolism and lay a solid foundation for engineering efforts toward valorizing C1 feedstocks.
Accelerometer-measured intensity-specific physical activity, genetic risk and incident type 2 diabetes: a prospective cohort study
Authors: Luo Mengyun , Yu Chenhao , Del Pozo Cruz Borja , Chen Liangkai , Ding Ding 
Published: June 2023

ObjectiveAlthough 30 min/day of moderate-intensity physical activity is suggested for preventing type 2 diabetes (T2D), the current recommendations exclusively rely on self-reports and rarely consider the genetic risk. We examined the prospective dose-response relationships between total/intensity-specific physical activity and incident T2D accounting for and stratified by different levels of genetic risk.MethodsThis prospective cohort study was based on 59 325 participants in the UK Biobank (mean age=61.1 years in 2013–2015). Total/intensity-specific physical activity was collected using accelerometers and linked to national registries until 30 September 2021. We examined the shape of the dose-response association between physical activity and T2D incidence using restricted cubic splines adjusted for and stratified by a polygenic risk score (based on 424 selected single nucleotide polymorphisms) using Cox proportional hazards models.ResultsDuring a median follow-up of 6.8 years, there was a strong linear dose-response association between moderate-to-vigorous-intensity physical activity (MVPA) and incident T2D, even after adjusting for genetic risk. Compared with the least active participants, the HRs (95% CI) for higher levels of MVPA were: 0.63 (0.53 to 0.75) for 5.3–25.9 min/day, 0.41 (0.34 to 0.51) for 26.0–68.4 min/day and 0.26 (0.18 to 0.38) for >68.4 min/day. While no significant multiplicative interaction between physical activity measures and genetic risk was found, we found a significant additive interaction between MVPA and genetic risk score, suggesting larger absolute risk differences by MVPA levels among those with higher genetic risk.ConclusionParticipation in physical activity, particularly MVPA, should be promoted especially in those with high genetic risk of T2D. There may be no minimal or maximal threshold for the benefits. This finding can inform future guidelines development and interventions to prevent T2D.
Strains ofFaecalibacterium prausnitziiand its extracts reduce blood glucose levels, percent HbA1c, and improve glucose tolerance without causing hypoglycemic side effects in diabetic and prediabetic mice
Authors: Kallassy John , Gagnon Emily , Rosenberg Dawn , Silbart Lawrence K , McManus Simon A 
Published: June 2023

IntroductionThe commensal bacteriumFaecalibacterium prausnitziiis a prominent member of the microbiome of animals and humans, and it plays an important role in several physiological processes. Numerous studies have correlated the reduction ofF. prausnitziiabundance with many disease states, including irritable bowel syndrome, Crohn’s disease, obesity, asthma, major depressive disorder, and metabolic diseases in humans. Studies have also correlatedF. prausnitziiwith diseases in humans involved in altered glucose metabolism, including diabetes.Research design and methodsThe aim of this study was to investigate the effects of compositions derived from three strains ofF. prausnitzii(coined FPZ) on glucose metabolism in diet-induced obese male C57BL/6J prediabetic and type 2 diabetic mice. The primary endpoints of these studies were measuring changes in fasting blood glucose, glucose tolerance (as measured by a glucose tolerance test), and percent hemoglobin A1c (HbA1c) with longer term treatment. Two placebo-controlled trials were carried out using both live cell FPZ and killed cell FPZ and extracts. Two additional placebo-controlled trials were carried out in non-diabetic mice and mice that previously had type 2 diabetes (T2D).ResultsBoth trials in prediabetic and diabetic mice revealed that peroral administration of live FPZ or extracts from FPZ lowered fasting blood glucose levels and improved glucose tolerance compared with control mice. A trial administering longer FPZ treatment also resulted in lowered percent HbA1c compared with control mice. Additionally, trials in non-diabetic mice treated with FPZ demonstrated that FPZ treatment does not lead to hypoglycemia.ConclusionsThe trial results have shown that treatment with different formulations of FPZ result in lower blood glucose levels, lower percent HbA1c, and improved glucose response in mice compared with control prediabetic/diabetic mice. FPZ is a promising candidate as an orally administered probiotic or postbiotic to manage and improve pre-diabetes and T2D.
Why urban communities from low-income and middle-income countries participate in public and global health research: protocol for a scoping review
Authors: Gagnon-Dufresne Marie-Catherine , Sarmiento Ivan , Fortin Geneviève , Andersson Neil , Zinszer Kate 
Published: June 2023

IntroductionAs the number of people living in cities increases worldwide, particularly in low-income and middle-income countries (LMICs), urban health is a growing priority of public and global health. Rapid unplanned urbanisation in LMICs has exacerbated inequalities, putting the urban poor at increased risk of ill health due to difficult living conditions in cities. Collaboration with communities in research is a key strategy for addressing the challenges they face. The objective of this scoping review is, therefore, to identify factors that influence the participation of urban communities from LMICs in public and global health research.Methods and analysisWe will develop a search strategy with a health librarian to explore the following databases: MEDLINE, Embase, Web of Science, Cochrane, Global Health and CINAHL. We will use MeSH terms and keywords exploring the concepts of ‘low-income and middle-income countries’, ‘community participation in research’ and ‘urban settings’ to look at empirical research conducted in English or French. There will be no restriction in terms of dates of publication. Two independent reviewers will screen and select studies, first based on titles and abstracts, and then on full text. Two reviewers will extract data. We will summarise the results using tables and fuzzy cognitive mapping.Ethics and disseminationThis scoping review is part of a larger project to be approved by the University of Montréal’s Research Ethics Committee for Science and Health in Montréal (Canada), and the Institutional Review Board of the James P Grant School of Public Health at BRAC University in Dhaka (Bangladesh). Results from the review will contribute to a participatory process seeking to combine scientific evidence with experiential knowledge of stakeholders in Dhaka to understand how to better collaborate with communities for research. The review could contribute to a shift toward research that is more inclusive and beneficial for communities.
Protocol for a systematic review and meta-analysis of the diagnostic test accuracy of host and HPV DNA methylation in cervical cancer screening and management
Authors: Bowden Sarah J , Ellis Laura Burney , Kalliala Ilkka , Paraskevaidi Maria , Tighe Jack , Kechagias Konstantinos S , Doulgeraki Triada , Paraskevaidis Evangelos , Arbyn Marc , Flanagan James , Veroniki Areti , Kyrgiou Maria 
Published: June 2023

IntroductionHuman papillomavirus (HPV) is necessary but not sufficient for cervical cancer development. During cervical carcinogenesis, methylation levels increase across host and HPV DNA. DNA methylation has been proposed as a test to diagnose cervical intraepithelial neoplasia (CIN); we present a protocol to evaluate the accuracy of methylation markers to detect high-grade CIN and cervical cancer.Methods and analysisWe will search electronic databases (Medline, Embase and Cochrane Library), from inception, to identify studies examining DNA methylation as a diagnostic marker for CIN or cervical cancer, in a cervical screening population. The primary outcome will be to assess the diagnostic test accuracy of host and HPV DNA methylation for high-grade CIN; the secondary outcomes will be to examine the accuracy of different methylation cut-off thresholds, and accuracy in high-risk HPV positive women. Our reference standard will be histology. We will perform meta-analyses using Cochrane guidelines for diagnostic test accuracy. We will use the number of true positives, false negatives, true negatives and false positives from individual studies. We will use the bivariate mixed effect model to estimate sensitivity and specificity with 95% CIs; we will employ different bivariate models to estimate sensitivity and specificity at different thresholds if sufficient data per threshold. For insufficient data, the hierarchical summary receiver operating curve model will be used to calculate a summary curve across thresholds. If there is interstudy and intrastudy variation in thresholds, we will use a linear mixed effects model to calculate the optimum threshold. If few studies are available, we will simplify models by assuming no correlation between sensitivity and specificity and perform univariate, random-effects meta-analysis. We will assess the quality of studies using QUADAS-2 and QUADAS-C.Ethics and disseminationEthical approval is not required. Results will be disseminated to academic beneficiaries, medical practitioners, patients and the public.PROSPERO registration numberCRD42022299760.
Surveillance towards preventing paediatric incidence of respiratory syncytial virus attributable respiratory tract infection in primary and secondary/tertiary healthcare settings in Merseyside, Cheshire and Bristol, UK
Authors: Fyles Fred , Hill Helen , Duncan Gregory , Carter Emma , Solórzano Carla , Davies Kelly , McLellan Lauren , Lesosky Maia , Dodd James , Finn Adam , McNamara Paul Stephen , Lewis David , Bangert Mathieu , Vassilouthis Natalya , Taylor Matthew , Ferreira Daniela M , Collins Andrea M 
Published: June 2023

IntroductionRespiratory syncytial virus (RSV) is a common respiratory virus, particularly affecting children, and can cause respiratory infections such as croup and bronchiolitis. The latter is a leading cause of paediatric hospitalisation within the UK. Children <3 years of age and/or with underlying health conditions are more vulnerable to severe RSV infection.There are currently limited data on the incidence of laboratory-confirmed RSV, particularly within primary care settings and outside the typical ‘RSV season’, which in the Northern hemisphere tends to coincide with winter months. There is also a lack of data on the health economic impact of RSV infection on families and healthcare systems.This observational surveillance study aims to collect data on the incidence of laboratory-confirmed RSV-attributable respiratory tract infection (RTI) in children aged <3 years presenting to primary, secondary or tertiary care; it also aims to estimate the health economic and quality of life impact of RSV-attributable infection in this cohort. Such data will contribute to informing public health strategies to prevent RSV-associated infection, including use of preventative medications.Methods and analysisParents/carers of children <3 years of age with RTI symptoms will consent for a respiratory sample (nasal swab) to be taken. Laboratory PCR testing will assess for the presence of RSV and/or other pathogens. Data will be obtained from medical records on demographics, comorbidities, severity of infection and hospitalisation outcomes. Parents will complete questionnaires on the impact of ongoing infection symptoms at day 14 and 28 following enrolment. The primary outcome is incidence of laboratory-confirmed RSV in children <3 years presenting to primary, secondary or tertiary care with RTI symptoms leading to health-seeking behaviours. Recruitment will be carried out from December 2021 to March 2023, encompassing two UK winter seasons and intervening months.Ethics and disseminationEthical approval has been granted (21/WS/0142), and study findings will be published as per International Committee of Medical Journal Editors’ guidelines.
Retrieval of distally migrated coil using stent retriever and proximal aspiration
Authors: Mendez-Ruiz Alan , Mendez Aldo A , Zevallos Cynthia B , Quispe Orozco Darko , Farooqui Mudassir , Samaniego Edgar A , Dandapat Sudeepta , Ortega-Gutierrez Santiago 
Published: June 2023

Endovascular coiling has become the preferred treatment of many centers for the management of both ruptured and unruptured aneurysms. Coil migration is a rare complication that can lead to vessel occlusion in 90% of the cases. Endovascular techniques for coil retrieval have shown less complication rates than open surgery. Stent retriever devices have been successfully used for the retrieval of proximally migrated coils, however, distally migrated coils still represent a challenge with greater risk of complications. In the present technical video 1, we demonstrate the successful retrieval of a distally M3 migrated coil using a 3 mm Trevo XP ProVue stent riever (Stryker Neurovascular, Fremont, CA, USA) in combination with proximal aspiration.Video 1
Improvements in workplace and household productivity with certolizumab
pegol treatment in axial spondyloarthritis: results to week 96 of a phase
III study
Authors: van der Heijde Désirée , Braun Jürgen , Rudwaleit Martin , Purcaru Oana , Kavanaugh Arthur F 
Published: June 2023

Objectives
To evaluate the effect of certolizumab pegol (CZP) on work and
household productivity, and on participation in family, social and
leisure activities in patients with axial spondyloarthritis (axSpA),
including ankylosing spondylitis (AS) and non-radiographic (nr-)
axSpA.

Methods
RAPID-axSpA (NCT01087762) was a phase III, double-blind,
placebo-controlled trial to week (Wk) 24, dose-blind to Wk48 and
open-label to Wk204. A total of 325 patients were randomised 1:1:1 to
placebo, CZP 200 mg Q2W or CZP 400 mg Q4W. The validated
arthritis-specific Work Productivity Survey assessed the impact of axSpA
on work and household productivity and participation in social
activities during the preceding month. Data are shown to Wk96, with
responses compared between treatment arms (placebo vs CZP 200 mg and
400 mg dose groups combined) and subpopulations using a non-parametric
bootstrap-t method.

Results
At baseline, 63.2% of placebo and 72.0% of CZP patients were
employed. By Wk24, CZP patients reported on average 1.0 fewer days of
absenteeism and 2.6 fewer days of presenteeism per month, compared with
0.4 and 0.9 fewer days for placebo. At home, by Wk24, CZP patients
reported on average 3.0 household work days gained per month versus 1.3
for placebo. CZP patients reported fewer days with reduced household
productivity or days lost for social participation. Similar improvements
were observed in AS and nr-axSpA subpopulations and improvements with
CZP were maintained to Wk96.

Conclusions
Compared with placebo, treatment with CZP significantly improved
work and household productivity and resulted in greater social
participation for patients with axSpA, which could lead to considerable
indirect cost gains.

Trial registration number
NCT01087762.
Characterisation of patients with axial psoriatic arthritis and patients with axial spondyloarthritis and concomitant psoriasis in the SCQM registry
Authors: Ciurea Adrian , Götschi Andrea , Kissling Seraphina , Bernatschek Alexander , Bürki Kristina , Exer Pascale , Nissen Michael J , Möller Burkhard , Scherer Almut , Micheroli Raphael 
Published: June 2023

BackgroundWithin the spectrum of spondyloarthritides, axial spondyloarthritis (axSpA) and psoriatic arthritis (PsA) present with overlapping features. Axial involvement in PsA (axial PsA) is treated according to recommendations for axSpA, as specific studies in axial PsA are scarce. We compared characteristics of patients with axSpA (particularly of patients with axSpA and concomitant psoriasis (pso)) with those of patients with axial PsA.MethodsPatients with axSpA and PsA in the Swiss Clinical Quality Management (SCQM) registry were included if information on pso and axial involvement was available. Patients with AxSpA were stratified by axSpA with and without pso (axSpA±pso) and patients with PsA were stratified to axial PsA or strictly peripheral PsA.ResultsPrevious or current psoriasis was observed in 479/4489 patients with axSpA (10.7%). Of 2631 patients with PsA, 1153 (43.8%) presented with axial involvement (opinion of the treating rheumatologist). Compared with patients with axSpA+pso, patients with axial PsA were older at symptom onset and at inclusion in SCQM, were less frequently HLA-B27 positive, had back pain less frequently and a higher prevalence of dactylitis and peripheral arthritis. A positive family history of pso or PsA was more frequent in axial PsA, while a positive family history of axSpA was more frequent in patients with axSpA+pso. Disease activity, function and mobility were comparable in axSpA+pso versus axial PsA.ConclusionPatients with axial PsA differ from patients with axSpA+pso in important demographic and clinical characteristics, and genetically, but present with a comparable disease burden. Treatment studies specifically dedicated to axial PsA seem warranted.
Better cigarette tax policies and higher tobacco excise tax revenues
Authors: Lee Hye Myung , Drope Jeffrey , Guerrero-López Carlos Manuel , Perucic Anne-Marie , Chaloupka Frank J 
Published: June 2023

Background

In November 2021, the Tobacconomics team published the second edition of the
Cigarette Tax Scorecard
which evaluates cigarette taxation in each country based on four components—cigarette price, affordability change, tax share and tax structure. This study examines the relationship between the overall cigarette tax score and tobacco excise tax revenue between 2014 and 2018.

Methods

Using cigarette tax scores from the
Tobacconomics Cigarette Tax Scorecard
and tobacco excise tax revenue information from WHO, this analysis is based on ordinary least squares estimations to assess the association between the overall cigarette tax scores and tobacco excise tax revenues per capita controlling for countries’ tobacco control environment, sociodemographic characteristics and country and year fixed effects.

Results
A 1-point higher overall cigarette tax score is associated with higher tobacco excise tax revenue per capita of $11.98 (in constant 2018 purchasing power parity international dollars). For low and middle-income countries and lower performing countries at baseline, a 1-point higher overall cigarette tax score is associated with higher tobacco excise tax revenue per capita of $11.32 and $6.92, respectively. If all countries had increased their scores to ‘5’, the tobacco excise tax revenue per capita would have increased by 22.51%.

Conclusions
Higher overall cigarette tax scores are associated with higher tobacco excise tax revenue per capita. Countries aiming to reach higher cigarette tax scores would be able to reduce tobacco use and increase their tobacco tax revenue, which can be allocated to development priorities.
Retailer experiences with tobacco sales bans: lessons from two early adopter jurisdictions
Authors: McDaniel Patricia A , Smith Elizabeth A , Malone Ruth E 
Published: June 2023

Background
Beverly Hills and Manhattan Beach, California, are the first two US cities to prohibit the sale of tobacco products, passing ordinances that went into effect on 1 January 2021. We sought to learn about retailers’ experiences with these laws 22 months after implementation.

Methods
Brief in-person interviews with owners or managers of businesses that formerly sold tobacco (n=22).

Results
Participant experiences varied by type of retailer. Managers at large chain stores reported no problems adapting to the law and little effect on overall sales. Many were largely indifferent to the sales bans. By contrast, most managers or owners of small, independent retailers reported losses of both revenue and customers, and expressed dissatisfaction with the laws. Small retailers in Beverly Hills objected particularly to exemptions that city made allowing hotels and cigar lounges to continue their sales, which they saw as undermining the health rationale for the law. The small geographical area covered by the policies was also a source of frustration, and retailers reported that they had lost business to retailers in nearby cities. The most common advice small retailers had for other retailers was to organise to oppose any similar attempts in their cities. A few retailers were pleased with the law or its perceived effects, including a reduction in litter.

Conclusion
Planning for tobacco sales ban or retailer reduction policies should include considering impacts on small retailers. Adopting such policies in as wide a geographical area as possible, as well as allowing no exemptions, may help reduce opposition.