bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calibration and Sensitivity Analysis of Macro and Meso Parameters of Discrete Element Model for Coal Measure Soil
Authors: Zhang Hong , Zheng Mingxin , Rong Yao , Cui Meng , Cheng Kun 
Published: June 2023

Abstract
The orthogonal test sequence of the meso parameters of the discrete element model was designed by using the orthogonal test method. The calculation method of directly determining the meso parameters from the macro mechanical parameters was established by using the test simulation calculation results and the multi factor nonlinear joint inversion method. The proposed method was applied to the discrete element numerical simulation of triaxial test of coal measure soil. The results show that the numerical simulation results are in good agreement with the stress-strain curves of the triaxial test of coal bearing soil. Through error analysis, it is found that the maximum error of the partial stress peak is 5.4%, the error of the cohesion is 2%, the error of the internal friction angle is 7%, and the error is all within 10%. It verifies that the method for rapid determination of the meso parameters proposed in this paper is feasible, and provides a new idea for the calibration of the meso parameters in the discrete element numerical simulation method.
Design of stress monitoring system for planetary gear shaft
Authors: Gao Chengang , Ma Xiaoping , Yue Yanjiong , Chen Kaiwen , Wang Dacheng , Song Menglin , Cui Hongbin 
Published: June 2023

Abstract
A remote sensing gear shaft stress monitoring system is studied to deal with the stress balance of transmission gear, which realizes the real-time dynamic monitoring of the planetary gear shaft stress. The design of the whole system structure, the installation position of the basic system and the special working environment of the gear are carried out; the circuit of each function unit is designed, which is based on the overall index requirement and installation space limitation; the software program design is carried out on the basis of the hardware circuit; The main components of the system and the principle of dynamic monitoring system are described; each functional unit and the whole of the system are tested and analyzed in detail. The operation results show that the design is reliable, the actual functions of each unit can meet the design index, and has a certain contribution in the field of gear shaft stress monitoring.
Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process
Authors: Adiyaman Recep , Edmunds Nicholas S , Genc Ahmet G , Alharbi Shuaa M A , McGuffin Liam J 
Published: June 2023

Abstract

Motivation
The accuracy gap between predicted and experimental structures has been significantly reduced following the development of AlphaFold2 (AF2). However, for many targets, AF2 models still have room for improvement. In previous CASP experiments, highly computationally intensive MD simulation-based methods have been widely used to improve the accuracy of single 3D models. Here, our ReFOLD pipeline was adapted to refine AF2 predictions while maintaining high model accuracy at a modest computational cost. Furthermore, the AF2 recycling process was utilized to improve 3D models by using them as custom template inputs for tertiary and quaternary structure predictions.

Results
According to the Molprobity score, 94% of the generated 3D models by ReFOLD were improved. AF2 recycling showed an improvement rate of 87.5% (using MSAs) and 81.25% (using single sequences) for monomeric AF2 models and 100% (MSA) and 97.8% (single sequence) for monomeric non-AF2 models, as measured by the average change in lDDT. By the same measure, the recycling of multimeric models showed an improvement rate of as much as 80% for AF2-Multimer (AF2M) models and 94% for non-AF2M models.

Availability and implementation
Refinement using AlphaFold2-Multimer recycling is available as part of the MultiFOLD docker package (https://hub.docker.com/r/mcguffin/multifold). The ReFOLD server is available at https://www.reading.ac.uk/bioinf/ReFOLD/ and the modified scripts can be downloaded from https://www.reading.ac.uk/bioinf/downloads/.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Revelation, Revolution and Utopia, c.1770–1820
Authors: Jones P M 
Published: June 2023

Abstract
The philosophes and France’s revolutionaries are often held jointly responsible for the attack on revealed religion in the course of the eighteenth century. This article suggests that the culture of belief among the laity of Protestant and Catholic Europe was not seriously undermined or even radically altered by the ralliement of State churches to the rationalistic and utilitarian values of the Enlightenment. Scepticism remained a narrowly confined phenomenon and religious ‘enthusiasm’, including literal belief in biblical prophecy, recovered strongly towards the century’s end. Traumatic public events (including the destruction of the Jesuit Order, the war in America, the revolution in France, the rise of Napoleon) were capable of triggering a latent millenarian reflex in nearly all social milieus. Although frequently played down by researchers, biblical literalism, prophetic witness and the quest for spiritual utopia should be considered an integral part of the tumultuous politics of the 1790 and 1800s. The article focuses particularly on the outlook and behaviour of England’s Rational Dissenters, French and Italian Jansenists and German Pietists in order to illustrate this contention. It concludes that, even at elite levels, detachment from religion was superficial and mainly doctrinal in nature. God, in one form or another, survived both the Enlightenment and the French Revolution.
Burden of mood symptoms and disorders in implantable cardioverter defibrillator patients: a systematic review and meta-analysis of 39 954 patients
Authors: Ghezzi Erica S , Sharman Rhianna L S , Selvanayagam Joseph B , Psaltis Peter J , Sanders Prashanthan , Astley Jack M , Knayfati Sara , Batra Vrinda , Keage Hannah A D 
Published: June 2023

Abstract

Aims
Implantable cardioverter defibrillators (ICDs) prevent sudden cardiac death. Anxiety, depression, and post-traumatic stress disorder (PTSD) are underappreciated symptoms. We aimed to systematically synthesize prevalence estimates of mood disorders and symptom severities, pre- and post-ICD insertions. Comparisons were made with control groups, as well as within ICD patients by indication (primary vs. secondary), sex, shock status, and over time.

Methods
Databases (Medline, PsycINFO, PubMed, and Embase) were searched without limits from inception to 31 August 2022; 4661 articles were identified, 109 (39 954 patients) of which met criteria.

Results
Random-effects meta-analyses revealed clinically relevant anxiety in 22.58% (95%CI 18.26–26.91%) of ICD patients across all timepoints following insertion and depression in 15.42% (95%CI 11.90–18.94%). Post-traumatic stress disorder was seen in 12.43% (95%CI 6.90–17.96%). Rates did not vary relative to indication group. Clinically relevant anxiety and depression were more likely in ICD patients who experienced shocks [anxiety odds ratio (OR) = 3.92 (95%CI 1.67–9.19); depression OR = 1.87 (95%CI 1.34–2.59)]. Higher symptoms of anxiety were seen in females than males post-insertion [Hedges’ g = 0.39 (95%CI 0.15–0.62)]. Depression symptoms decreased in the first 5 months post-insertion [Hedges’ g = 0.13 (95%CI 0.03–0.23)] and anxiety symptoms after 6 months [Hedges’ g = 0.07 (95%CI 0–0.14)].

Conclusion
Depression and anxiety are highly prevalent in ICD patients, especially in those who experience shocks. Of particular concern is the prevalence of PTSD following ICD implantation. Psychological assessment, monitoring, and therapy should be offered to ICD patients and their partners as part of routine care.
Additional coils mitigate elevated defibrillation threshold in right-sided implantable cardioverter defibrillator generator placement: a simulation study
Authors: Qian Shuang , Monaci Sofia , Mendonca-Costa Caroline , Campos Fernando , Gemmell Philip , Zaidi Hassan A , Rajani Ronak , Whitaker John , Rinaldi Christopher A , Bishop Martin J 
Published: June 2023

Abstract

Aims
The standard implantable cardioverter defibrillator (ICD) generator (can) is placed in the left pectoral area; however, in certain circumstances, right-sided cans may be required which may increase defibrillation threshold (DFT) due to suboptimal shock vectors. We aim to quantitatively assess whether the potential increase in DFT of right-sided can configurations may be mitigated by alternate positioning of the right ventricular (RV) shocking coil or adding coils in the superior vena cava (SVC) and coronary sinus (CS).

Methods and results
A cohort of CT-derived torso models was used to assess DFT of ICD configurations with right-sided cans and alternate positioning of RV shock coils. Efficacy changes with additional coils in the SVC and CS were evaluated. A right-sided can with an apical RV shock coil significantly increased DFT compared to a left-sided can [19.5 (16.4, 27.1) J vs. 13.3 (11.7, 19.9) J, P &lt; 0.001]. Septal positioning of the RV coil led to a further DFT increase when using a right-sided can [26.7 (18.1, 36.1) J vs. 19.5 (16.4, 27.1) J, P &lt; 0.001], but not a left-sided can [12.1 (8.1, 17.6) J vs. 13.3 (11.7, 19.9) J, P = 0.099). Defibrillation threshold of a right-sided can with apical or septal coil was reduced the most by adding both SVC and CS coils [19.5 (16.4, 27.1) J vs. 6.6 (3.9, 9.9) J, P &lt; 0.001, and 26.7 (18.1, 36.1) J vs. 12.1 (5.7, 13.5) J, P &lt; 0.001].

Conclusion
Right-sided, compared to left-sided, can positioning results in a 50% increase in DFT. For right-sided cans, apical shock coil positioning produces a lower DFT than septal positions. Elevated right-sided can DFTs may be mitigated by utilizing additional coils in SVC and CS.
Fast-track virtual reality software to facilitate 3-dimensional reconstruction in congenital heart disease
Authors: Bertelli Francesco , Raimondi Francesca , Godard Charlotte , Bergonzoni Emma , Cattapan Claudia , Gastino Elisa , Galliotto Francesco , Boddaert Nathalie , El Beheiry Mohamed , Masson Jean-Baptiste , Guariento Alvise , Vida Vladimiro L 
Published: June 2023

Abstract

OBJECTIVES
Two limitations of the clinical use of 3-dimensional (3D) reconstruction and virtual reality systems are the relatively high cost and the amount of experience required to use hardware and software to effectively explore medical images. We have tried to simplify the process and validate a new tool developed for this purpose with a novel software package.

METHODS
Five patients with right partial anomalous pulmonary venous return with adequate preoperative images acquired with magnetic resonance imaging were enrolled. Five volunteers with no previous experience in the field of 3D reconstruction were instructed to use the software after viewing a short video tutorial. Users were then asked to create a 3D model of each patient's heart using DIVA software. Their results were compared quantitatively and qualitatively with a benchmark reconstruction performed by an experienced user.

RESULTS
All our participants recreated 3D models in a relatively short time, maintaining a good overall quality (average quality score ≥ 3 on a scale of 1–5). The overall trend of all the parameters analysed showed a statistical improvement between case 1 and case 5, as users became more and more experienced.

CONCLUSIONS
DIVA is a simple software program that allows accurate 3D reconstruction in a relatively short time (“fast-track” virtual reality). In this study, we demonstrated the potential use of DIVA by inexperienced users, with a significant improvement in quality and time after a few cases were performed. Further studies are needed to confirm the potential application of this technology on a larger scale.
Exergetic-energetic effectiveness of a simple H2O-LiBr absorption chiller operated by solar energy collected using a direct flow evacuated tube collector
Authors: Al-Tahaineh Hamza A 
Published: June 2023

Abstract
A comprehensive examination of a 10-kW simple H2O/LiBr absorption system energized by an evacuated tube solar collector of the single-ended glass direct flow type has been conducted. For various operating conditions, the thermal and exergetic performance coefficients (COP, ECOP respectively), and exergy destruction (ΔE) through each system component are determined. At evaporator temperatures of 1°C, 5°C, and 10°C, COP around 0.75, 0.77, and 0.81, respectively, was achieved, and the maximum ECOP values of approximately 0.36, 0.35, and 0.342, respectively, could be attained. The highest values of COP and ECOP were seen at a desorber temperature of around 90°C. Around 41% of the system’s exergy destructed were attributed to the desorber. The lowest absorber exergy losses occur at a desorber temperature of 90°C for various evaporator temperatures. Increasing the desorber temperature by a factor of two reduces the system’s efficiency from 0.45 to 0.20. In addition, 65.88% solar collector exegetic efficiency was achieved when its differential temperature surpasses 50°C.
O02 Patterns of GP and nurse-independent prescriber prescriptions for antibiotics dispensed in the community in England: a retrospective analysis
Authors: Courtenay Molly , Gillespie David , Lim Rosemary 
Published: June 2023

Abstract

Background
The substitution of nurses for doctors is a strategy used in primary care to improve access to, and efficiency and quality of, care. Many of these nurses prescribe medicines including antibiotics.

Objectives
To identify nurse-independent prescriber (NIP) and GP numbers in England, the proportions and types of NIPs and GP antibiotic prescriptions dispensed in the community, and the impact of COVID-19 on the volume, rate and types of antibiotic prescriptions dispensed.

Methods
A descriptive population-based retrospective cohort study using data obtained from the National Health Service Business Service Authority (under a Freedom of Information request) on GP and nurse-independent prescriber prescriptions for antibiotics dispensed in the community in England between January 2014 and October 2021.

Results
Between 2014 and 2021, the number of NIPs (headcount) in England almost doubled from 24 457 to 41 649. Of the 41 649 NIPs in 2021, the prescriptions of 34 997 (84%) were dispensed in the community, i.e. a rise of 146% over this 6-year period. By contrast, GP numbers (headcount) rose by 10% to 44 681. Of the 25.373 million antibiotic prescriptions dispensed between 2014 and 2021, NIPs were responsible for 8.6%. The rate of dispensed antibiotic prescriptions decreased (NIPs by 50% and GPs by 21%) between 2014 and 2020 (where data across the full year were available). This decreasing trend continued following the onset of the pandemic across both groups. In line with guidance for the treatment of minor infections, narrow-spectrum antibiotics (penicillins, macrolides and tetracyclines) were the most frequently dispensed across both NIPs and GPs. Trends in prescription of antibiotics during the pandemic were reflected in the use of individual classes of antibiotics prescribed for RTIs.

Conclusions
Given the rising numbers of nurse prescribers and their increasing contributory influence on total antibiotic prescribing, it is important that this group is included in antimicrobial stewardship efforts. NIPs prescribe fewer antibiotics than GPs but work under different conditions (e.g. longer consultations and less complex patients), and so, interventions should also be tailored to this group and the population and context in which they are delivered.
O04 Understanding the key role of accessory genes in AMR phenotype through interpretable machine learning techniques
Authors: Dillon Lucy , Dimonaco Nicholas J , Creevey Christopher J 
Published: June 2023

Abstract

Background
Antimicrobial resistance (AMR) genes are found to be ubiquitous within the microbiome, even when antimicrobial usage is absent. To identify the AMR phenotype, the most common method is to use a laboratory-based assay. Yet, when dealing with samples from the microbiome, many species are difficult to culture within the laboratory. The vast quantity of strains would be time-consuming to culture. To avoid this, a computational approach may be a more favourable choice. AMR gene finder tools are efficient at determining the AMR genotype. Despite this, how a genotype relates to the AMR phenotype is still an open question.

Methods
To evaluate the relationship between the AMR phenotype and the AMR genotype, 16 950 genomes from BV-BRC which had corresponding MIC values were analysed. Using Weka’s J48 decision tree model, the relationship between the AMR phenotype and the AMR genotype was analysed. The role of accessory genes in relation to the AMR phenotype was analysed in the same way.

Results
The J48 models could predict the AMR phenotype accurately using AMR genes and accessory genes; the average accuracy was 91.7% and 92.2%, respectively. The results found that gene co-occurrence, presence and absence of genes are key factors to analyse when identifying the AMR phenotype from genomic data. These factors are not evaluated by commonly used AMR gene finder tools, which could miss vital information to determine the correct phenotype.

Conclusions
Our results highlight why we should continue to research the relationship between the AMR phenotype and genomic data.
P01 Antibiotic efficacy treatment of community-acquired pneumonia among CMV-infected individuals
Authors: Chichirelo-Konstantynovych Kiarina , Konstantynovych Tetyana 
Published: June 2023

Abstract

Background
The investigation is devoted to possible antibiotic resistance formation and its adverse event prognostic influence among young patients with community-acquired pneumonia (CAP) with cytomegalovirus (CMV) persistence and absence of other comorbid pathology.

Subjects and methods
The observation included 105 patients (average age 34.1 ± 0.8 years), which had been examined by epidemiological, clinical (including PORT prognostic scale) according to European Respiratory Society requirements, serological test for CMV IgM, IgG detection and antibiotic usage questionnaire for a 3-month period prior CAP.

Results
76.2% (n = 80) CAP patients had positive CMV IgG. CMV-positive patients were characterized by higher severity outcome risk in the nearest future versus CMV-negative ones (P &lt; 0.0001): third risk class—14.9 times higher, fourth risk class—10.5 times higher. CMV IgG–positive results correlated with the CAP severity level (r (Spearman) = 0.472). In total, 51.4% (n = 54, among them 47 CMV-positive patients) mentioned antibiotic use during the last 3 months prior to CAP. During the CAP treatment, 75.0% (n = 60) of CMV-positive patients and 20.0% (n = 5) of CMV-negative ones did not respond to antibiotic treatment by cephalosporin and quinolone lines and needed changes in aetiology prescription according to antibiotic susceptibility microbial test. 61.3% (n = 47) of CAP patients (everybody was after medication replacement) got adverse events like antibiotic-associated diarrhoea (16 cases), QT prolongation in ECG (17 cases), creatinine, urea elevation (11 cases) and alanine/aminotransferase elevation (5 cases).

Conclusions
CMV persistence is associated with higher risk of severe CAP among young patients without comorbid pathologies and contributes to the antibiotic resistance creation as well as related side effects.
P03 A retrospective review of the safety and efficacy of dalbavancin at Ireland’s largest acute medical hospital
Authors: Conlon Peter , Murphy Aisling , McKernan Sarah , Williamson Clare , Kelly Mary , Bannan Ciaran 
Published: June 2023

Abstract

Background
Dalbavancin is a second-generation lipoglycopeptide antibiotic. It is licensed in Ireland and the United Kingdom for the management of acute skin and soft tissue infections. International colleagues report treatment success in its use for patients who are unable to stay in hospital for prolonged periods and not suitable for OPAT.1 We reviewed the use of dalbavancin at St. James’s Hospital, Dublin, which is the largest hospital in Ireland with over 700 acute beds. We are located in Dublin’s inner city which experiences significant socio-economic deprivation.

Methods
We used the electronic patient records at St. James’s Hospital to capture all uses of dalbavancin from August 2018 to September 2022. We established baseline demographics, indication, microbiological characteristics, if there was oversight by ID/micro, safety and treatment outcomes. We considered how many hospital days were saved if a patient was changed to dalbavancin and discharged home compared with how long they would have required to stay in hospital to pursue conventional treatment. One hospital day in an acute bed is estimated to cost 800€.

Results
We identified 23 patients who met the inclusion criteria. Baseline demographics are shown in Table 1. The most common indication was endovascular infection (35%) and skin and soft tissue infection (35%) (Figure 1). Most patients were not bacteraemic. Staphylococcus aureus was the most common organism identified on blood culture (Figure 2). In total, 322 hospital beds were saved, which equates to 257 600 EUR. No patients had an adverse drug reaction. 100% of cases were discussed with micro or ID.

Conclusions
Dalbavancin is a safe and effective drug. It is another tool that can be used when caring for patients who are experiencing unstable housing and challenging social circumstances. Our experience has found 0 adverse events, 69% of patients experienced treatment success (this increases to 88.8% if we exclude those lost to follow up). This is an important finding considering 17% of indications were considered ‘on label’. Dalbavancin can save money on hospital beds and also reduces non-recyclable plastic associated with repeated doses of IV antibiotics.