bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteriological and molecular characterization of temperature- and CO
2
-dependent
Streptococcus pneumoniae
serotype 24F ST162 isolated from Japanese children
Authors: Kobayashi Jun , Ohkusu Misako , Matsumoto Takehisa , Kubota Noriko , Ishiwada Naruhiko 
Published: October 2023

ABSTRACT

Streptococcus pneumoniae
serotype 24F is one of the most prevalent non-vaccine serotypes that causes invasive pneumococcal disease (IPD) in many countries, including Japan. This study aimed to analyze the bacteriological and molecular characteristics of serotype 24F sequence type (ST) 162, which has been increasingly isolated from pediatric patients with IPD in Japan recently. The examination of growth conditions, sequencing of genes associated with the CO
2
dependence, and antimicrobial susceptibility testing at 35°C under 5% CO
2
were performed for 10 isolates obtained from Japanese children with IPD caused by serotype 24F ST162. All isolates failed to grow at 35°C in ambient air; however, they showed growth at 30°C in ambient air and at 35°C under 5% CO
2
. Sequencing of
murF
involved in cell wall synthesis indicated that all isolates had a single amino acid substitution, MurF
A179V
. Additionally, all isolates were sensitive to penicillin G and resistant to trimethoprim-sulfamethoxazole. Furthermore, 25 non-capnophilic strains were obtained from all CO
2
-dependent isolates, and their
murF
sequences were compared. Thirteen of the 25 non-capnophilic strains displayed a different amino acid substitution, MurF
V179A
, whereas the other 12 presented the previously described MurF
A179V
. This suggests that a proportion of the CO
2
-dependent phenotype of serotype 24F ST162 may have been conferred by MurF
A179V
; however, the mechanism for the CO
2
dependence of these isolates warrants further investigation. The CO
2
-dependent serotype 24F ST162 pneumococcal isolates shared common characteristics in terms of growth patterns, molecular basis, and antimicrobial susceptibility; therefore, future epidemiological trends of this clone must be closely monitored.

IMPORTANCE

We characterized
Streptococcus pneumoniae
serotype 24F sequence type (ST) 162 isolated from Japanese children with invasive pneumococcal disease (IPD). Owing to its highly invasive nature, serotype 24F is expected to be isolated from clinically significant cases. Serotype 24F ST162 isolates tested in the present study did not grow at 35°C in ambient air. Therefore, antimicrobial susceptibility testing using the broth microdilution method, which is usually conducted in ambient air, cannot be performed, posing a clinical challenge. Clinical practitioners and laboratory personnel should be aware of the epidemiological, bacteriological, and molecular characteristics of serotype 24F ST162. We believe that our findings can help diagnose and treat IPD caused by serotype 24F ST162, a serotype expected to become problematic in the post-13 valent pneumococcal conjugate vaccine era.
Hybrid RNA sequencing of broad bean wilt virus 2 from faba beans
Authors: Maina Solomon , Norton Sally L. , Rodoni Brendan C. 
Published: October 2023

ABSTRACT

High-throughput sequencing (HTS) is an important tool for plant virus detection and discovery. HTS technologies such as Nanopore sequencing has been rapidly developing in recent years, and offers new possibilities for fast routine diagnostic applications. This study compared MiSeq (Illumina) RNA-Seq with the MinION sequencer (Oxford Nanopore Technologies) (ONT) direct-RNA-Seq methods to detect and sequence the broad bean wilt virus 2 (BBWV2) genome. The Illumina BBWV2 RNA1 and RNA2 genome segments were intact and matched with ONT with 99.1% and 98.8% nucleotide identity (nt) match, respectively. The RNA1 genome derived from ONT had deletions within the nucleoside-triphosphate binding and protease factor open-reading frames, and the upstream of five untranslated regions. However, its RNA2 was intact, and no sequencing errors were observed. The ONT and Illumina RNA1 and RNA 2 BBWV2 genome segments clustered together phylogenetically along with other none-
Fabaceae
species, BBWV2 RNA1 NCBI accession
KC790225
, and RNA 2
MW556592
both from China. This is the first BBWV2 genome study reported in Australia and forms part of the strategy to integrate versatile diagnostic genomics tools at the border to safeguard the Australian grains industry.

IMPORTANCE
Globally, viral diseases impair the growth and vigor of cultivated crops such as grains, leading to a significant reduction in quality, marketability, and competitiveness. As an island nation, Australia has a distinct advantage in using its border to prevent the introduction of damaging viruses, which threaten the continental agricultural sector. However, breeding programs in Australia rely on imported seeds as new sources of genetic diversity. As such, it is critical to remain vigilant in identifying new and emerging viral pathogens, by ensuring the availability of accurate genomic diagnostic tools at the grain biosecurity border. High-throughput sequencing offers game-changing opportunities in biosecurity routine testing. Genomic results are more accurate and informative compared to traditional molecular methods or biological indexing. The present work contributes to strengthening accurate phytosanitary screening, to safeguard the Australian grains industry, and expedite germplasm release to the end users.
Microbisporicin (NAI-107) protects
Galleria mellonella
from infection with
Neisseria gonorrhoeae
Authors: Hofkens Nele , Gestels Zina , Abdellati Said , De Baetselier Irith , Gabant Philippe , Martin Anandi , Kenyon Christopher , Manoharan-Basil Sheeba Santhini 
Published: October 2023

ABSTRACT

Due to the increasing incidence of antibiotic-resistant bacterial pathogens, the need for the development of alternative compounds is of utmost importance. Bacteriocins are considered a promising alternative to antibiotics. In this study, we determined the
in vitro
activities of 65 bacteriocins from the PARAGEN collection along with microbisporicin (NAI-107) against 14 WHO reference isolates of
Neisseria gonorrhoeae
, one isolate of
Neisseria meningitidis
, and four commensal
Neisseria
spp. The initial screening of the bacteriocins was carried out using a spot-on-lawn assay wherein 12 bacteriocins (12/66) showed a zone of inhibition against the WHO-P
N. gonorrhoeae
isolate. Four bacteriocins (4/12), Garvicin KS (GarKS) (ABC), lacticin (lcn) Q, lcn Z, and NAI-107, demonstrated higher activity, and minimum inhibitory concentrations (MICs) using agar dilutions were determined for 19
Neisseria
spp. GarKS (ABC), lcn Q, and lcn Z had an MIC range of 4–16 µg/mL, whereas NAI-107 had an MIC range of <0.25 to 2 µg/mL. Using an
in vivo Galleria mellonella
model, we determined the efficacy of GarKS (ABC), lcn Z, and NAI-107. GarKS (ABC) and lcn Z displayed no
in vivo
toxicity but showed no
in vivo
activity against WHO-P
N. gonorrhoeae
. In contrast, NAI-107 was as effective as ceftriaxone and significantly increased the survival rate of WHO-P
N. gonorrhoeae
-infected
G. mellonella
larvae. In conclusion, NAI-107 exhibited potent
in vitro
and
in vivo
activities against
N. gonorrhoeae
. To our knowledge, this is the first study to demonstrate that NAI-107 possesses anti-gonococcal activity
in vivo
.

IMPORTANCE

We screened 66 bacteriocins to see if they exhibited anti-gonococcal activity. We found 12 bacteriocins with anti-gonococcal effects, and 4 bacteriocins showed higher anti-gonococcal activity. Three bacteriocins, lacticin Z, lacticin Q, and Garvicin KS (ABC), showed
in vitro
anti-gonococcal activity but no
in vivo
inhibitory effects against the
Neisseria gonorrhoeae
(WHO-P) isolate. On the other hand, NAI-107 showed
in vivo
anti-gonococcal activity. The findings suggest that NAI-107 is a promising alternative to treat gonorrhea infections.
Establishment of prediction models to predict survival among patients with cervical cancer based on socioeconomic factors: a retrospective cohort study based on the SEER Database
Authors: Jia Xiaoping , Zhou Jing , Fu Yanyan , Ma Cailing 
Published: October 2023

ObjectiveTo construct and validate predictive models based on socioeconomic factors for predicting overall survival (OS) in cervical cancer and compare them with the American Joint Council on Cancer (AJCC) staging system.DesignRetrospective cohort study.Setting and participantsWe extracted data from 5954 patients who were diagnosed with cervical cancer between 2007 and 2011 from the Surveillance, Epidemiology, and End Results Database. This database holds data related to cancer incidence from 18 population-based cancer registries in the USA.Outcome measures1-year and 5-year OS.ResultsOf the total 5954 patients, 5820 patients had 1-year mortality and 5460 patients had 5-year mortality. Lower local education level [Hazard ratios (HR): 1.15, 95% confidence interval (CI): 1.04 to 1.27, p= 0.005] and being widowed (HR 1.28, 95% CI 1.06 to 1.55, p=0.009) were associated with a worse OS for patients with cervical cancer. Having insurance (HR 0.75, 95% CI 0.62 to 0.90, p=0.002), earning a local median annual income of ≥US$56 270 (HR 0.83, 95% CI 0.75 to 0.92, p<0.001) and being married (HR 0.79, 95% CI 0.69 to 0.89, p<0.001) were related to better OS in patients with cervical cancer. The predictive models based on socioeconomic factors and the AJCC staging system had a favourable performance for predicting OS in cervical cancer compared with the AJCC staging system alone.ConclusionOur proposed predictive models exhibit superior predictive performance, which may highlight the potential clinical application of incorporating socioeconomic factors in predicting OS in cervical cancer.
Second opinion and time to knee arthroplasty: a prospective cohort study of 142 patients
Authors: Kisch Rebecca , Grill Eva , Müller Martin , Pietzner Jens , Paulus Alexander C , Weigl Martin 
Published: October 2023

ObjectiveThe objective of this study was to determine the impact of obtaining a second opinion consultation on time to knee arthroplasty (KA). We further examined the frequency of KA and the determinants of KA following the second opinion.DesignProspective cohort study.SettingThe second opinion programme was implemented at the Ludwig Maximilian University Hospital in Munich.ParticipantsParticipants comprised patients with knee osteoarthritis who were insured with one of the largest statutory health insurance Allgemeine Ortskrankenkasse Bayern (mean age 64.3±9.6 years). Patients participated in a second-opinion programme and completed questionnaires on site before and after personal presentation for the second opinion consultation. Follow-up questionnaires were delivered by post at 3 and 12 months after the second opinion consultation. Of the 142 patients included in the study, 47 (33.1%) underwent KA within 12 months after obtaining the second opinion.Primary outcome measuresPrimary outcome measure was time until patients received KA. Cox proportional hazard modelling was used to calculate the associations between the selected predictors and time that elapsed between receipt of the second opinion to KA.ResultsMean time until KA was 17 weeks. Kaplan-Meier curves showed significant differences in time to KA according to the recommendation given at second opinion consultation, knee-related quality of life and Kellgren-Lawrence grade. In multivariate Cox proportional hazard modelling, second opinion recommendation (HR 5.33, 95% CI 1.16, 24.41) and knee-related quality of life (HR 1.03, 95% CI 1.01, 1.06) were significant predictors of time from second opinion to KA.ConclusionsObtaining a second opinion had significant impact on time to knee replacement. Those who were recommended immediate surgery also underwent surgery more quickly after the second opinion. The effect of knee-related quality of life supports the importance of patient-reported outcome measures in the decision for or against KA.
Evaluating kidney function and the associated risk factors among patients with type 2 diabetes mellitus: a cross-sectional study at a tertiary hospital in Jordan
Authors: Al-Momany Abass , Almomani Ensaf Y , Almomani Huda Y , Al-Azzam Sayer I , Qablan Ahmad 
Published: October 2023

BackgroundThe diabetes prevalence is escalating in Jordan; as a consequence, the risk of developing diabetic kidney diseases is also increasing.ObjectiveThis study evaluated the effect of risk factors and comorbidities on kidney function in patients with type 2 diabetes mellitus (T2DM).DesignA cross-sectional, survey-based study.SettingParticipants were recruited from the endocrinology and cardiology clinics of a tertiary hospital in Jordan.ParticipantsPatients with T2DM aged 18 years and more who had undergone a kidney function test within a year before data collection.Outcome measuresThe estimated GFR (eGFR) mean values and proteinuria presence were used to evaluate the impact of risk factors on kidney function. Descriptive and analytical statistical approaches were used to calculate mean, prevalence and correlations. The SPSS software was used with a p value<0.05 for significance.ResultsOf the total 331 study participants, 54.1% were men and 45.9% were women. The mean age was 60 years. The eGFR mean values were significantly reduced in patients with T2DM with hypertension, hyperlipidaemia and proteinuria (p<0.01). The correlation analysis results showed that the eGFR was positively correlated with hypertension and hyperlipidaemia presence (rs=0.253, 0.220), and negatively correlated with age, body mass index and diabetes duration (rs=−0.395, –0.151, −0.221), respectively. However, the eGFR did not corelate with income, sex, smoking and anaemia. Of note, about 68% of the patients with T2DM had uncontrolled diabetes.ConclusionsKidney function were severely affected in patients with T2DM in the presence of risk factors and comorbidities. It is highly recommended to control diabetes through medications and life style, and to regularly check for kidney function to halt the deteriorations in kidney function.
Myocardial infarction and physical function: the REasons for Geographic And Racial Differences in Stroke prospective cohort study
Authors: Levitan Emily B , Goyal Parag , Ringel Joanna Bryan , Soroka Orysya , Sterling Madeline R , Durant Raegan W , Brown Todd M , Bowling C Barrett , Safford Monika M 
Published: October 2023

ObjectiveTo examine associations between myocardial infarction (MI) and multiple physical function metrics.MethodsAmong participants aged≥45 years in the REasons for Geographic And Racial Differences in Stroke prospective cohort study, instrumental activities of daily living (IADL), activities of daily living (ADL), gait speed, chair stands and Short Form-12 physical component summary (PCS) were assessed after approximately 10 years of follow-up. We examined associations between MI and physical function (no MI (n=9472), adjudicated MI during follow-up (n=288, median 4.7 years prior to function assessment), history of MI at baseline (n=745), history of MI at baseline and adjudicated MI during follow-up (n=70, median of 6.7 years prior to function assessment)). Models were adjusted for sociodemographic characteristics, health behaviours, depressive symptoms, cognitive impairment, body mass index, diabetes, hypertension and urinary albumin to creatinine ratio. We examined subgroups defined by age, gender and race.ResultsThe average age at baseline was 62 years old, 56% were women and 35% were black. MI was significantly associated with worse IADL and ADL scores, IADL dependency, chair stands and PCS, but not ADL dependency or gait speed. For example, compared with participants without MI, IADL scores (possible range 0–14, higher score represents worse function) were greater for participants with MI during follow-up (difference: 0.37 (95% CI 0.16 to 0.59)), MI at baseline (0.26 (95% CI 0.12 to 0.41)) and MI at baseline and follow-up (0.71 (95% CI 0.15 to 1.26)), p<0.001. Associations tended to be greater in magnitude among participants who were women and particularly black women.ConclusionMI was associated with various measures of physical function. These decrements in function associated with MI may be preventable or treatable.
The role of physiology in the contemporary management of coronary artery disease
Authors: Rubino Francesca , Pompei Graziella , Brugaletta Salvatore , Collet Carlos , Kunadian Vijay 
Published: October 2023

Coronary physiology assessment, including epicardial and microvascular investigations, is a fundamental tool in the contemporary management of patients with coronary artery disease. Coronary revascularisation guided by functional evaluation has demonstrated superiority over angiography-only-guided treatment. In patients with chronic coronary syndrome, revascularisation did not demonstrate prognostic advantage in terms of mortality over optimal medical therapy (OMT). However, revascularisation of coronary stenosis, which induces myocardial ischaemia, has demonstrated better outcome than OMT alone. Pressure wire (PW) or angiography-based longitudinal coronary physiology provides a point-by-point analysis of the vessel to detect the atherosclerotic pattern of coronary disease. A careful evaluation of this disease pattern allows clinicians to choose the appropriate management strategy.Patients with diffuse disease showed a twofold risk of residual angina after percutaneous coronary intervention (PCI) than those with focal disease. Therefore, OMT alone or coronary artery bypass graft might be considered over PCI. In addition, the post-PCI physiological assessment aims to optimise the result revealing residual myocardial ischaemia. Improvement in post-PCI PW or angiography-based functional indices has been associated with better quality of life and reduced risk of cardiac events and residual angina. Therefore, the information obtained from coronary physiology allows for an optimised treatment strategy, which ultimately leads to improve patient’s prognosis and quality of life. This review provides an overview of the latest available evidence in the literature regarding the use of functional assessment of epicardial coronary stenosis in different settings in the contemporary patient-tailored management of coronary disease.
Echocardiographic estimation of pulmonary pressure in patients with severe tricuspid regurgitation
Authors: Lemarchand Léo , Auffret Vincent , Le Breton Hervé , Bedossa Marc , Boulmier Dominique , Galli Elena , Donal Erwan , Leurent Guillaume 
Published: October 2023

ObjectivesThe estimation of systolic pulmonary artery pressure (sPAP) by transthoracic echocardiography (TTE) is challenging in patients with severe tricuspid regurgitation (TR). The study aimed to determine the reliability of the assessment of sPAP by TTE in this population.MethodsThis study was a single-centre analysis of consecutive patients at the University Hospital of Rennes with right heart catheterisation and TTE, performed with a maximum delay of 48 hours. Lin’s concordance coefficient (LCC) and Bland-Altman analysis were used to compare the values.ResultsAfter applying the exclusion criteria, 236 patients were included in the analysis (age 71±11.5 years old; male 56%). The two principal indications were TR (34.3%) and mitral regurgitation (32.2%). The correlation between the two procedures was good in the total population (LCC=0.80; 95% limits of agreement (LOA): 0.74, 0.84), but weaker in the 78 patients (33%) with severe TR (LCC=0.67; 95% LOA: 0.49, 0.80), with a propensity to an underestimation by TTE. An elevated right atrial pressure (RAP) was associated with an underestimation by TTE of about 8 mmHg. The presence of a ‘V-wave cut-off’ sign on continuous-wave Doppler (OR=3.74; 95% CI 1.48, 9.30; p<0.01), found exclusively in patients with severe TR, was an independent predictor of sPAP misestimation by TTE.ConclusionThe reliability of the estimation of sPAP in patients with severe TR could be altered by high RAP which cannot be estimated with current thresholds.
Peak oxygen consumption by smartwatches compared with cardiopulmonary exercise test in complex congenital heart disease
Authors: Tran Tomio , Steiner Jill Marie , Venkateswaran Aparajithan , Buber Jonathan 
Published: October 2023

ObjectiveTo evaluate for correlation between exercise capacity as assessed by peak oxygen consumption (pVO2) measurement during a cardiopulmonary exercise test (CPET) and smartwatches reporting this parameter in patients with adult congenital heart disease (ACHD) complex lesions.MethodsA prospective study that included patients with ACHD either a Fontan circulation or a right ventricle supporting the systemic circulation who underwent two separate CPETs at least 1 year apart. Generalised estimating equations linear regression was performed to identify factors associated with correlation between smartwatch and CPET-derived pVO2.Results48 patients (71% with a Fontan circulation, 42% females, mean age 33±9 years) underwent two CPETs between May 2018 and May 2022 with echocardiograms performed within 6 months of each CPET. Apple Watch was the predominant smartwatch used (79%). Smartwatch and CPET measured peak heart rate (Pearson correlation=0.932, 95% CI (0.899, 0.954)) and pVO2(0.8627, 95% CI (0.8007, 0.9064) and 0.8634, 95% CI (0.7676, 0.9215) in the first and second CPET, respectively) correlated well, with smartwatch-measured pVO2values measuring higher by a mean of 3.146 mL/kg/min (95% CI (2.559, 3.732)). Changes in pVO2between the first and the second CPET also correlated well (Pearson correlation=0.9165, 95% CI (0.8549, 0.9525)), indicating that for every 1 mL/(min kg) change in CPET-measured pVO2, there was a corresponding 0.896 mL/(min kg) change in the smartwatch-measured pVO2.ConclusionBoth absolute values and changes over time in pVO2as measured by smartwatches and CPETs correlate well in patients with complex ACHD.
Nutritional support in palliative cancer care: quality of life in oral versus tube feeding
Authors: Santos Larissa Pereira , Calixto-Lima Larissa , de Oliveira Livia Costa , Wiegert Emanuelly Varea Maria 
Published: October 2023

BackgroundNutritional support (NS) offered through oral nutritional supplements (ONS) or enteral nutrition (EN) and its impact on quality of life (QoL) is a controversial topic in patients with cancer receiving palliative care (PC).AimsTo compare the QoL of patients without and with use of NS, including ONS or EN in patients with incurable cancer receiving PC.MethodsCross-sectional analysis with patients that were evaluated at PC Unit between June 2021 and February 2023. QoL was assessed using the Quality of Life Questionnaire Core 15. Patients were classified into three groups according to the NS: ONS (n=72; 33%), EN (n=61; 28%) and control group (CG) (n=87; 39%), the last one being formed by patients not using NS. Adjusted logistic regression models were used to verify the association of the domains of QoL with the type of NS.ResultsA total of 220 patients were included, with a median age of 64 (58–70) years, predominantly male (54.1%). The EN group had worse scores in physical function when compared with the ONS group (p=0.037) and appetite loss when compared with the CG (p=0.013). The ONS (OR: 2.70; 95% CI 1.32 to 5.49) and EN groups (OR: 2.61; 95% CI 1.24 to 5.49) were independently associated with a higher chance of presenting appetite loss in relation to the CG.ConclusionIn general, there was no difference in the QoL of patients using NS when compared with patients not using NS. However, patients using NS have more chance of having appetite loss.