bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome sequence of
Asaia bogorensis
strain SC1 isolated from an
Aedes aegypti
mosquito crop
Authors: Chakraborty Souvik , Benoit Joshua B. , Rowe Annette R. , Sackett Joshua D. 
Published: October 2023

ABSTRACT

Understanding microbe-host interactions is key to combating disease transmission by mosquitoes. Here, we report the genome sequence of
Asaia bogorensis
strain SC1 isolated from a human-blood-fed
Aedes aegypti
mosquito crop. Metabolic pathway characteristics of aerobic respiration were present in the genome, along with multiple putative antibiotic resistance mechanisms.
Complete sequence of the genome-reduced
Escherichia coli
DGF-298
Authors: Matteau Dominick , Champie Antoine , Grenier Frédéric , Rodrigue Sébastien 
Published: October 2023

ABSTRACT

We report the complete genome sequence and annotation of
Escherichia coli
DGF-298, a genome-reduced
E. coli
strain with interesting properties for systems and synthetic biology. DGF-298 has a single circular chromosome of 2,991,126 bp and 2,831 genes, including 2,691 coding sequences, with a mean G + C content of ~51%.
Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO
Authors: Carrasco Muriel Jorge , Long Christopher , Sonnenschein Nikolaus 
Published: October 2023

ABSTRACT

Genome-scale metabolic (GEM) models are knowledge bases of the reactions and metabolites of a particular organism. These GEM models allow for the simulation of the metabolism, for example, calculating growth and production yields—based on the stoichiometry, reaction directionality, and uptake rates of the metabolic network. Over the years, several extensions have been added to take into account other actors in metabolism, going beyond pure stoichiometry. One such extension is enzyme-constrained models, which enable the integration of proteomics data into GEM models containing the necessary
k
cat
values for their enzymes. Given its relatively recent formulation, there are still challenges in standardization and data reconciliation between the model and the experimental measurements. In this work, we present geckopy 3.0 (genome-scale model with enzyme constraints, using Kinetics and Omics in Python), an actualization from scratch of the previous Python implementation of the same name. This update tackles the aforementioned challenges, to reach maturity in enzyme-constrained modeling. With the new geckopy, proteins are typed in the Systems Biology Markup Language (SBML) document, taking advantage of the SBML Groups extension, in compliance with community standards. In addition, a suite of relaxation algorithms—in the form of linear and mixed-integer linear programming problems—has been added to facilitate the reconciliation of raw proteomics data with the metabolic model. Several functionalities to integrate experimental data were implemented, including an interface layer with pytfa for the usage of thermodynamics and metabolomics constraints. Finally, the relaxation algorithms were benchmarked against public proteomics data sets in
Escherichia coli
for different conditions, revealing targets for improving the enzyme-constrained model and/or the proteomics pipeline.

IMPORTANCE
The metabolism of biological cells is an intricate network of reactions that interconvert chemical compounds, gathering energy, and using that energy to grow. The static analysis of these metabolic networks can be turned into a computational model that can efficiently output the distribution of fluxes in the network. With the inclusion of enzymes in the network, we can also interpret the role and concentrations of the metabolic proteins. However, the models and the experimental data often clash, resulting in a network that cannot grow. Here, we tackle this situation with a suite of relaxation algorithms in a package called geckopy. Geckopy also integrates with other software to allow for adding thermodynamic and metabolomic constraints. In addition, to ensure that enzyme-constrained models follow the community standards, a format for the proteins is postulated. We hope that the package and algorithms presented here will be useful for the constraint-based modeling community.
Comparative study of widefield swept-source optical coherence tomography angiography in eyes with concomitant age-related macular degeneration and diabetic retinopathy
Authors: Finn Matthew , Baldwin Grace , Garg Itika , Wescott Hannah E , Koch Thomas , Vingopoulos Filippos , Zeng Rebecca , Choi Hanna , Sayah Diane , Husain Deeba , Patel Nimesh A , Kim Leo A , Miller Joan W , Wu David M , Vavvas Demetrios G , Miller John B 
Published: October 2023

Background/aims
We sought to evaluate widefield swept-source optical coherence tomography angiography (WF SS-OCTA) among eyes with concomitant age-related macular degeneration (AMD) and diabetes mellitus or diabetic retinopathy (DM/DR).

Methods
This cross-sectional, comparative study consisted of three study groups: eyes with (1) AMD and DM/DR, (2) AMD alone and (3) DM/DR alone. WF SS-OCTA (3×3, 6×6 and 12×12 mm) images were captured. Vascular metrics included foveal avascular zone (FAZ), vessel density (VD) and vessel skeletonised density (VSD). Mixed-effects multivariable regression models adjusted for age were performed by cohort and subgroup based on AMD and DR stages.

Results
Our cohort included 287 eyes from 186 patients with an average age of 64±14.0 years old. Results revealed significantly reduced vascular metrics in concomitant AMD and DM/DR eyes (N=68) compared with AMD-only eyes (N=71) on all angiograms but not compared with DM/DR-only eyes (N=148). For example, when compared with AMD-only eyes, AMD and DM/DR eyes had significantly reduced VD (β=−0.03, p=0.016) and VSD (β=−1.09, p=0.022) on 12×12 mm angiograms, increased FAZ perimeter (β=0.51, p=0.025) and FAZ area (β=0.11, p=0.015) on 6×6 mm angiogram, and reductions in all VD and VSD metrics on 3×3 and 6×6 mm angiograms. However, only 3×3 mm angiogram FAZ metrics were significantly different when comparing DM/DR eyes with concomitant AMD and DM/DR eyes.

Conclusion
WF SS-OCTA revealed significant reductions in retinal microvasculature metrics in AMD and DM/DR eyes compared with AMD-only eyes but not compared with DM/DR-only eyes.
Predictors and prognosis of population-based subjective cognitive decline: longitudinal evidence from the Caerphilly Prospective Study (CaPS)
Authors: Ball Harriet A , Coulthard Elizabeth , Fish Mark , Bayer Antony , Gallacher John , Ben-Shlomo Yoav 
Published: October 2023

ObjectivesTo understand associations between the subjective experience of cognitive decline and objective cognition. This subjective experience is often conceptualised as an early step towards neurodegeneration, but this has not been scrutinised at the population level. An alternative explanation is poor meta-cognition, the extreme of which is seen in functional cognitive disorder (FCD).DesignProspective cohort (Caerphilly Prospective Study).SettingPopulation-based, South Wales, UK.ParticipantsThis men-only study began in 1979; 1225 men participated at an average age of 73 in 2002–2004, including assessments of simple subjective cognitive decline (sSCD, defined as a subjective report of worsening memory or concentration). Dementia outcomes were followed up to 2012–2014. Data on non-completers was additionally obtained from death certificates and local health records.Primary and secondary outcome measuresThe primary outcome measure was incident dementia over 10 years. Secondary outcome measures included prospective change in objective cognition and cross-sectional cognitive internal inconsistency (the existence of a cognitive ability at some times, and its absence at other times, with no intervening explanatory factors except for focus of attention).ResultssSCD was common (30%) and only weakly associated with prior objective cognitive decline (sensitivity 36% (95% CI 30 to 42) and specificity 72% (95% CI 68 to 75)). Independent predictors of sSCD were older age, poor sleep quality and higher trait anxiety. Those with sSCD did not have excess cognitive internal inconsistency, but results suggested a mild attentional deficit. sSCD did not predict objective cognitive change (linear regression coefficient −0.01 (95% CI −0.13 to 0.15)) nor dementia (odds ratio 1.35 (0.61 to 2.99)) 10 years later.ConclusionssSCD is weakly associated with prior objective cognitive decline and does not predict future cognition. Prior sleep difficulties and anxiety were the most robust predictors of sSCD. sSCD in the absence of objective decline appears to be a highly prevalent example of poor meta-cognition (ie, poor self-awareness of cognitive performance), which could be a driver for later FCD.
Association between WeChat use and mental health among middle-aged and older adults: a secondary data analysis of the 2020 China Family Panel Studies database
Authors: Zhang Chong , Liang Xiaolin 
Published: October 2023

ObjectiveThis study focused on the association between WeChat use, the most popular social software in China, and the mental health of middle-aged and older adults.DesignNationwide cross-sectional study.SettingThe China Family Panel Studies (CFPS) database.ParticipantsThe study sample included 11 127 middle-aged and elderly people aged 45 and above identified from the 2020 CFPS database.ResultsWeChat usage was negatively associated with depression (OR: 0.782, p<0.01), as was the WeChat Moments sharing (OR: 0.846, p<0.01). 10.310% of the relationship between WeChat usage and depression came from the effects of interpersonal relationships (5.720%) and social trust (4.590%), with significant indirect effects (B=−0.028, p<0.01). Sixteen per cent of the relationship between WeChat Moments sharing and depression came from the effect of interpersonal relationships (6.800%) and social trust (9.200%), and the indirect effect was also significant (B=−0.032, p<0.01).ConclusionsWeChat use may empower middle-aged and elderly to maintain close social relationships and trust contributing to their mental health.
Professional stakeholders’ expectations for the future of community pharmacy practice in England: a qualitative study
Authors: Paloumpi Evgenia , Ozieranski Piotr , Watson Margaret C , Jones Matthew D 
Published: October 2023

ObjectivesTo explore the views of professional stakeholders on the future of community pharmacy services in England. Specific objectives related to expectations of how community pharmacy services will be provided by 2030 and factors that will influence this.DesignQualitative, using semistructured interviews in person or via telephone/Skype. The topic guide was informed by a recent policy review that used the Walt and Gilson policy framework. Transcripts were analysed using inductive thematic analysis.SettingEngland.ParticipantsExternal stakeholders were representatives of non-pharmacy organisations, including policy-makers, commissioners and representatives of healthcare professions. Internal stakeholders were community pharmacists or pharmacy organisation representatives. Interviewees were identified using stakeholder mappingResultsIn total, 25 interviews were completed (7 external stakeholders and 18 internal stakeholders, of which 10 were community pharmacists). Community pharmacy was recognised as having a key role in expanding health system capacity (‘…pharmacy is the obvious person to take on those roles…’), particularly for long-term condition management (eg, adherence, reducing polypharmacy, monitoring), urgent care (eg, minor illnesses) and public health (including mental health). For these contributions to be developed and optimised, greater integration and collaboration with general practices will be needed (‘…there is no room for isolationism in pharmacy anymore…’), as well as use of technology in a patient-centred way and full access to health records. These changes will require workforce development together with appropriate commissioning and contractual arrangements. Community pharmacy is currently undervalued (‘…the complete misunderstanding by senior Government officials is very scary’) and recent investment in general practice pharmacists rather than community pharmacy was seen as a missed opportunity.ConclusionsCommunity pharmacy as a sector could and should be developed to increase health service capacity to address its current challenges. Numerous modifications are required from a range of stakeholders to create the environment in which these changes can occur.
Effectiveness of atosiban in women with previous single implantation failure undergoing frozen-thawed blastocyst transfer: study protocol for a randomised controlled trial
Authors: Cai He , Liu Shan , Chen Lijuan , Xie Jinlin , Yang Chen , Li Wentao , Mol Ben W , Shi Juanzi 
Published: October 2023

BackgroundUterine contractions may interfere with embryo implantation in assisted reproductive technology. To reduce these contractions and improve success rates, the oxytocin antagonist atosiban has been suggested for administration during embryo transfer. The aim of this study is to evaluate the effectiveness of atosiban in increasing live birth rates among women who have previously experienced a single implantation failure and are scheduled for single blastocyst transfer.Methods and analysisWe conduct a single-centre randomised controlled study comparing atosiban and placebo in women undergoing a single blastocyst transfer with a previous failed blastocyst transfer. Women with endocrine or systemic illnesses, recurrent miscarriages, uterine malformations or fibroids, untreated hydrosalpinx, endometriosis (stage III or IV) or uterine fibroids, as well as women undergoing preimplantation genetic testing, are ineligible. The primary outcome is live birth resulting from the frozen-thawed embryo transfer. Secondary outcomes include biochemical/clinical pregnancy, miscarriage, ectopic pregnancy, multiple pregnancies as well as maternal and perinatal outcomes. We plan to recruit 1100 women (550 women per group). This will allow us to demonstrate or refute an increase in live birth rate from 40% to 50%. Data analysis will follow the intention-to-treat principle. We will measure patterns of uterine peristalsis which will allow subgroup analysis for women with or without uterine peristalsis.Ethics and disseminationThis study has been approved by the Institutional Review Board of Northwest Women’s and Children’s Hospital (No. SZ2019001). Written informed consent will be obtained from each participant before randomisation. The results of the trial will be presented at scientific meetings and reported in publications.Trial registration numberChiCTR1900022333.
Risk factors associated with elevated intraocular pressure: a population-based study in a rural community of Bangladesh
Authors: Sharfuddin Ahmed Md , Ullah ABM Yasin , Barman Nilima , Ratan Zubair Ahmed , Mostafa Subarna , Khaleque Abdul , Kabir Showkat , Khan Maruf Haque , Haque M Atiqul 
Published: October 2023

ObjectiveHigh intraocular pressure (IOP) is one of the major modifiable risk factors for glaucoma. The objective was to examine socio-demographic and clinical factors related to IOP.Methods and analysisThis study was conducted among 3097 adults residing in a rural area of Bangladesh, with all participants undergoing clinical and ophthalmological evaluations. The measurement of IOP was carried out using of a rebound Tonometer called Icare pro. Multiple logistic regression analysis was employed to identify variables associated to IOP levels of 21 mm Hg or above. Adjusted OR (aOR) and 95% CI were reported.ResultsThis study found that, in total, 9% of the study population had high IOP in one or both eyes. Elevated IOP was significantly associated with respondents who were service holders (aOR 2.52; 95% CI 1.48 to 4.31), had a lower education level (aOR 1.55, 95% CI 1.07 to 2.23), used biomass fuel (aOR 2.00; 95% CI 1.09 to 3.67), belonged to a higher socioeconomic position (aOR 1.55, 95% CI 1.07 to 2.23) and had obesity (aOR 2.00; 95% CI 1.07 to 3.73), hypertension (aOR 1.32; 95% CI 1.01 to 1.73) or history of diabetes (aOR 2.44; 95% CI 1.67 to 3.55), after adjusting for covariates including age, sex, marital status, light source and tobacco consumption, in a multiple regression analysis.ConclusionChronic diseases, such as hypertension and diabetes, obesity and sociodemographic characteristics such as high socioeconomic status and use of biomass fuels, have all been linked to elevated IOP. Patients with chronic diseases should undergo for IOP testing regularly.
Implications of isolated white matter abnormalities on neonatal MRI in congenital CMV infection: a prospective single-centre study
Authors: Vande Walle Caroline , Keymeulen Annelies , Oostra Ann , Schiettecatte Eva , Dhooge Ingeborg Johanna , Smets Koenraad , Herregods Nele 
Published: October 2023

ObjectiveInvestigating the clinical implications of isolated white matter abnormalities on neonatal brain MRI in congenital cytomegalovirus (CMV).DesignProspective, observational.Patients/interventionsTwo paediatric radiologists, blinded to clinical data, independently scored the white matter in 286 newborns with congenital CMV. After assessing interobserver variability, mean score was used to categorise white matter (normal, doubtful or abnormal). Patients with other brain abnormalities were excluded.Main outcome measuresHearing and neuromotor evaluation.ResultsCohen’s weighted kappa was 0.79 (95% CI 0.73 to 0.84). White matter was normal in 121 patients, doubtful in 62, abnormal in 28. Median clinical follow-up was 12.0 months (IQR 12.0–27.7 months). Neonatal hearing loss occurred in 4/27 patients (14.8%) with abnormal, 1/118 patients (0.8%) with normal and 1/62 patients (1.6%) with doubtful white matter (p<0.01). Impaired cognitive development was seen in 3/27 patients (11.1%) with abnormal, 3/114 patients (2.6%) with normal and 1/59 patients (1.7%) with doubtful white matter (p=0.104). Alberta Infant Motor Scale (AIMS) was below P75 in 21/26 patients (80.8%) with abnormal, 73/114 patients (64.0%) with normal and 36/57 patients (63.2%) with doubtful white matter (p=0.231). In a subgroup of patients with minimal clinical follow-up of 18 months, AIMS score was below P75 in 10/13 patients (76.9%) with abnormal, 13/34 patients (38.2%) with normal and 7/20 patients (35.0%) with doubtful white matter (p<0.05).ConclusionsAbnormal white matter was associated with neonatal hearing loss and mild, lower motor scores. A tendency towards impaired cognitive development was seen. Patients with doubtful white matter did not show worse clinical outcome.
Calculator for predicting the probability of faculty promotion in an academic medical centre
Authors: Yeo May May , Lim Shih-Hui , Kumar Anshul , Thompson Anne W 
Published: October 2023

ObjectiveThe academic medical centre (AMC), with over 2200 faculty members, annually manages approximately 300 appointments and promotions. Considering these large numbers, we explored whether machine learning could predict the probability of obtaining promotional approvals.MethodsWe examined variables related to academic promotion using predictive analytical methods. The data included candidates’ publications, the H-index, educational contributions and leadership or service within and outside the AMC.ResultsOf the five methods employed, the random forest algorithm was identified as the ‘best’ model through our leave-one-out cross-validation model evaluation process.ConclusionsTo the best of our knowledge, this is the first study on the AMC. The developed model can be deployed as a ‘calculator’ to evaluate faculty performance and assist applicants in understanding their chances of promotion based on historical data. Furthermore, it can act as a guide for tenure and promotion committees in candidate review processes. This increases the transparency of the promotion process and aligns faculty aspirations with the AMC’s mission and vision. It is possible for other researchers to adopt the algorithms from our analysis and apply them to their data.
Home emergency response team for the seriously ill palliative care patient: feasibility and effectiveness
Authors: Deniau Nicolas , Shojaei Taraneh , Georges Alexandre , Danis Jean , Czapiuk Georges , Mercier Stephane , Maari Claudine , Pourchet Sylvain , Balladur Elisabeth , Leclaire Clement 
Published: October 2023

ObjectivesTo characterise trajectories associated with a new team organisation combining critical care and palliative care approaches at home.MethodsWe describe the pattern of an emergency response team 24/7 directed to patients with advanced illness presenting a distressing symptom at home, who wanted to stay at home and for whom hospitalisation was considered inappropriate by a shared medical decision-making process in an emergency situation. To assess preliminary impact of this Programme, we conducted a descriptive study on all consecutive patients receiving this intervention during the first year (between 6 September 2021 and 5 September 2022).ResultsAmong the 352 patients included, main advanced illnesses were cancer (41%), dementia (28%) or chronic organ failure (10%). They were critically ill with acute failures: respiratory (52%), neurological (48%) or circulatory (20%). Main distressing symptoms were breathlessness (43%) and pain (17%). Median response time from call to home-visit (IQR) was 140 (90–265) min. Median length of follow-up (IQR) was 4 (2–7) days. Main outcomes were death at home (72%), improvement (19%) or hospitalisation (9%) including three visits to emergency department (1%).ConclusionsOur study supports that shared decision-making process and urgent care at home are feasible and might prevent undesired hospitalisations.
Does probiotic ingestion reduce the risk of preeclampsia? A systematic review
Authors: Valiati Nayara , Puel Esthela M. , Stefani Cristine M. , Lataro Renata M. 
Published: October 2023

We aimed to systematically review the literature on the effects of probiotic consumption on the risk of preeclampsia (PE) development. Eight databases, clinical trial registries, and grey literature were searched until February 2022. Studies were included if they (1) were randomized clinical trials (RCTs), (2) included pregnant women aged ≥ 18 years old, (3) used probiotics products, and (4) were written in the Latin alphabet. A random-effects meta-analysis was performed using the risk ratio as the effect measure with 95% confidence intervals (CI) for PE. The search strategy identified 359 records, from which six RCTs were included. The six RCTs evaluated pregnant women with comorbidities and enrolled 593 women that received probiotics and 625 receiving placebo. None of the included RCTs analyzed healthy women. Probiotics increased by 12% the PE risk (RR 1.12, 95% CI, CI = 0.83–1.53, p = 0.46, χ2 = 3.31, df = 5 ( p = 0.65), I2 = 0%). The certainty of the evidence, evaluated through the Grading of Recommendations Assessment, Development and Evaluation approach, was rated as very low. In conclusion, probiotics supplementation may slightly increase PE rates in pregnant women with comorbidities. The risk may be higher in obese women and for periods of ingestion longer than eight weeks. However, the evidence certainty is very low. PROSPERO registration No.CRD42021278611.