bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of the LifeScale automated rapid phenotypic antimicrobial susceptibility testing on Gram-negative rods directly from positive blood cultures
Authors: Snyder James W. , Chaudhry Nadia , Hoffmann Wesley 
Published: October 2024

ABSTRACT

Rapid antimicrobial susceptibility testing (rAST) performed directly from blood cultures is essential to influencing the selection of appropriate antibiotics, preferably targeted therapy, for the treatment of bloodstream infections. Affinity Biosensors has developed the LifeScale, a phenotypic rAST system based on microfluidic sensors with a mechanical resonator that measures the mass of individual microbes. The combination of replication, biomass, and population profiling of individual microbes is analyzed to produce rAST results. The performance of the LifeScale was evaluated and compared to our current standard of care (SOC) antimicrobial susceptibility testing (AST) system under clinical conditions. The results indicated that the LifeScale is easy to use and provides rapid, reliable, and accurate AST results in less than 5 h directly from from positive blood cultures containing Gram-negative organisms listed in the current database. For all organism–antibiotic combinations involving polymicrobial cultures, LifeScale showed a resistant result when either mixed isolate was resistant. If these results prove to be robust on further testing, this may justify the reporting of rapid LifeScale results without the need for additional confirmatory testing.

IMPORTANCE
This is the first clinical-based study of a unique technology using microfluidic sensors to generate rapid antimicrobial susceptibility test results directly from blood cultures containing Gram-negative rods. The issue of polymicrobial cultures was also addressed in this study, which, to our knowledge, has not been addressed in publications of other rapid phenotypic AST systems. Overall, LifeScale results compared favorably with the SOC in terms of overall agreement, especially categorical agreement.
Fine-tuned spatiotemporal dynamics of DNA replication during phage lambda infection
Authors: Yu Zihao , Guan Jingwen , Hanson Catherine , Duong Trish , Zeng Lanying 
Published: October 2024

ABSTRACT

After the ejection of viral DNA into the host cytoplasm, the temperate bacteriophage (phage) lambda integrates a cascade of expressions from various regulatory genes, coupled with DNA replication, to commit to a decision between lysis and lysogeny. Higher multiplicity of infection (MOI) greatly shifts the decision toward the lysogenic pathway. However, how the phage separates the MOI from replicated viral DNA during lysis–lysogeny decision-making is unclear. To quantitatively understand the role of viral DNA replication, we constructed a reporter system facilitating the visualization of individual copies of phage DNA throughout the phage life cycle, along with the lysis–lysogeny reporters. We showed that intracellular viral DNA diverges between the lytic and lysogenic pathways from the early phase of the infection cycle, mostly due to the synchronization and success of DNA injection, as well as the competition for replication resources, rather than the replication rate. Strikingly, we observed two distinct replication patterns during lysogenization and surprisingly heterogeneous integration kinetics, which advances our understanding of temperate phage life cycles. We revealed that the weak repression function of Cro is critical for an optimal replication rate and plays a crucial role in establishing stable lysogens.

IMPORTANCE
Temperate bacteriophages, such as lambda, incorporate environmental cues including host abundance and nutrient conditions to make optimal decisions between propagation and dormancy. A higher phage-to-host ratio or multiplicity of infection (MOI) during λ infection strongly biases toward lysogeny. However, a comprehensive understanding of this decision-making process and the impact of phage replication prior to the decision is yet to be achieved. Here, we used fluorescence microscopy to quantitatively track the spatiotemporal progression of viral DNA replication in individual cells with different cell fates. The implementation of this fluorescent reporter system and quantitative analysis workflow opens a new avenue for future studies to delve deeper into various types of virus–host interactions at a high resolution.
PF-00835231 broadly inhibits swine Alpha-coronavirus, including emerging SADS-CoV
Authors: Shi Lei , Duan Yueyue , Cao Liyan , Zhang Yu , Yuan Cong , Sun Maowen , Zhang Juan , Kong Xiangyu , Zheng Haixue , Wang Qi 
Published: October 2024

ABSTRACT

Swine Alpha-coronaviruses are one of the most destructive pathogens affecting the swine industries across the world. Swine Alpha-coronaviruses include transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus, porcine respiratory coronavirus, and swine acute diarrhea syndrome coronavirus (SADS-CoV). Thus far, swine Alpha-coronaviruses treatment options are very limited. Therefore, the identification of safe and effective treatment of swine Alpha-coronaviruses is urgently needed. In the current study, we screened a library of 240 FDA-approved compounds for antiviral activity against TGEV. Among screening, the 3CL protease inhibitor PF-00835231 was shown to dramatically inhibit TGEV replication
in vitro
systems. Mechanistically, PF-00835231 inhibits nonstructural protein 5 (Nsp5) protease activity targeting the cleavage at Nsp5–Nsp6 of TGEV. Additionally, PF-00835231 exhibited the potent broad-spectrum swine Alpha-coronaviruses antiviral activity. Treatment of PF-00835231 in mice not only blocks SADS-CoV deadly infection but also dramatically reduces viral copies. Taken together, our study provides evidence that PF-00835231 may control of the current swine Alpha-coronaviruses and emerging swine Alpha-coronaviruses in the future.

IMPORTANCE
The COVID-19 pandemic has induced tremendous efforts to develop therapeutic strategies that target Beta-coronavirus including SARS-CoV-2. 3CL protease of Beta-coronavirus has been as a drug target for developing antiviral drugs. However, 3CL protease is not conserved in Alpha-coronavirus and Beta-coronavirus with only 44% amino acid similarity. Therefore, an inhibitor that prevents Alpha-coronaviruses infection is urgently needed. Swine Alpha-coronaviruses are one of the most destructive pathogens affecting the swine industries across the world. Swine herds with coronavirus diarrhea showed a high rate of co-infection between different Alpha-coronavirus. Our study, for the first time, showed that PF-00835231 inhibits swine Alpha-coronavirus infection. At the mechanistic level, we experimentally identified that PF-00835231 inhibits nonstructural protein 5 (Nsp5) protease activity targeting the cleavage at Nsp5–Nsp6 of Alpha-coronaviruses.
From flow to furnace: Low viscosity of three-phase lavas measured at Kīlauea 2018 eruption conditions
Authors: Halverson Brenna A. , Whittington Alan 
Published: November 2024

Abstract
Melt composition, temperature, and crystallinity are often seen as the three most important characteristics driving lava rheology, which controls eruptive behavior. Traditional methods of measuring the viscosity of crystallizing basalts often yield different mineral characteristics to natural samples and are typically bubble-free. To quantify the viscosity of basalts inclusive of bubble and crystal cargo, we developed a new technique to measure high-temperature three-phase isothermal lava viscosity and applied it to samples from the 2018 eruption of Kīlauea. This new experimental technique begins at subliquidus temperatures, preserving original phenocrysts. A short experimental duration allows for the retention of most of the original bubble population (19%–31% vs. 36% in the original lava) and accurate replication of crystal textures from field samples, as documented in quenched postexperiment samples. The observed rheological behavior in these experiments, conducted at syneruptive temperatures (1150–1105 °C) and strain rates (0.4–18 s–1), should therefore be representative of the lava flows. We measured average viscosities of 116 Pa·s at 1150 °C to 167 Pa·s at 1115 °C (i.e., only 10%–25% higher than calculated liquid viscosities at those temperatures) and a maximum of 1800 Pa·s at 1105 °C. These results are much lower than viscosity measured in traditional bubble-free experiments, which plateaued at ~14,000 Pa·s at 1115 °C. Our results suggest the effect of bubbles in three-phase magmas may be greater than predicted by models based on two-phase bubbly liquids, and this effect must be included in realistic lava flow rheology models. The method proposed here supplies a framework for providing the necessary experimental constraints.
In vivo lacrimal gland imaging artefact assessment based on swept-source optical coherence tomography for dry eye disease
Authors: Cheng Weijing , Li Longyue , Chen Juejing , Chen Ziyan , Li Jing , Liu Siyi , Zhang Nuan , Gu Feng , Wang Wenhui , Wang Wei , Yang Boyu , Liang Lingyi 
Published: November 2024

BackgroundThis study aimed to characterise imaging artefacts in the lacrimal gland using swept-source optical coherence tomography (SS-OCT) in patients with dry eye disease (DED) and healthy participants and identify risk factors for these artefacts.MethodsIn total, 151 eyes, including 104 from patients with DED and 47 from non-DED participants, were analysed. Demographic data collection, comprehensive ocular examinations and SS-OCT imaging of the palpebral lobe of the lacrimal gland were performed. Artefacts were classified into distinct categories with different severities. Univariate and multivariate logistic regression analyses were performed to evaluate the association of age, gender, best-corrected visual acuity, intraocular pressure (IOP) and the presence of DED with the presence of artefacts.ResultsEight artefact types and severity grading were defined by analysing 1208 lacrimal SS-OCT images. The three most prevalent artefacts were defocus (75.83%), cliff (67.47%) and Z-off (58.44%). The presence of artefacts was significantly associated with the presence of DED (OR=9.13; 95% CI, 2.39 to 34.88; p=0.001) and higher IOP (OR=1.34; 95% CI, 1.14 to 1.58; p<0.001). Furthermore, multivariate logistic analyses showed that lower tear film breakup time (OR=0.71; 95% CI, 0.55 to 0.92; p=0.009) and higher meibum quality score (OR=2.86; 95% CI, 1.49 to 5.48; p=0.002) were significantly associated with higher odds for the presence of artefacts.ConclusionsDED eyes had more SS-OCT image artefacts than normal eyes. Stringent standardised image quality control should be implemented before further image analysis when using SS-OCT to assess lacrimal gland image.
Seroprevalence of seven arboviruses of public health importance in sub-Saharan Africa: a systematic review and meta-analysis
Authors: Bangoura Salifou Talassone , Sidibé Sidikiba , Kaba Lanceï , Mbaye Aminata , Hounmenou Castro Gbêmêmali , Diallo Alhassane , Camara Saidouba Cherif , Diaby Maladho , Kadio Kadio Jean-Jacques Olivier , D’Ortenzio Eric , Camara Alioune , Vanhems Philippe , Delamou Alexandre , Delaporte Eric , Keita Alpha-Kabinet , Ottmann Michèle , Touré Abdoulaye , Khanafer Nagham 
Published: November 2024

BackgroundThe arboviruses continue to be a threat to public health and socioeconomic development in sub-Saharan Africa (SSA). Seroprevalence surveys can be used as a population surveillance strategy for arboviruses in the absence of treatment and vaccines for most arboviruses, guiding the public health interventions. The objective of this study was to analyse the seroprevalence of arboviruses in SSA through a systematic review and meta-analysis.MethodsWe searched PubMed/MEDLINE, Web of Science, Embase, Scopus and ScienceDirect databases for articles published between 2000 and 2022 reporting the seroprevalence of immunoglobulin G (IgG) antibodies to seven arboviruses in various human populations residing in SSA. The included studies were assessed using the checklist for assessing the risk of bias in prevalence studies, and the data were extracted using a standard form. A random effects model was used to estimate pooled seroprevalences. The potential sources of heterogeneity were explored through subgroup analyses and meta-regression. The protocol had been previously registered on International Prospective Register of Systematic Reviews with the identifier: CRD42022377946.ResultsA total of 165 studies from 27 countries, comprising 186 332 participants, were included. Of these, 141 were low-risk and 24 were moderate-risk. The pooled IgG seroprevalence was 23.7% (17.9–30.0%) for Chikungunya virus, 22.7% (17.5–28.4%) for dengue virus, 22.6% (14.1–32.5%) for West Nile virus, 16.4% (7.1–28.5%) for yellow fever virus, 13.1% (6.4–21.7%) for Zika virus, 9.2% (6.5–12.3%) for Rift Valley fever virus and 6.0% (3.1–9.7) for Crimean–Congo haemorrhagic fever virus. Subgroup and meta-regression analyses showed that seroprevalence differed considerably between countries, study populations, specific age categories, sample sizes and laboratory methods.ConclusionThis SRMA provides information on the significant circulation of various arboviruses in SSA, which is essential for the adoption and planning of vaccines. These findings suggest the need to invest in surveillance and research activities on arbovirus in SSA countries to increase our understanding of their epidemiology to prevent and respond to future epidemics.
Impact of BMI on fertility in an otherwise healthy population: a systematic review and meta-analysis
Authors: Turner Florence , Powell Simon G , Al-Lamee Hannan , Gadhvi Anjali , Palmer Ellen , Drakeley Andrew , Sprung Victoria S , Hapangama Dharani , Tempest Nicola 
Published: November 2024

BackgroundAn increased body mass index (BMI) can lead to subfertility; however, current literature fails to exclude the effect of other confounding medical conditions, raising questions regarding the direct link between increased BMI and fertility outcomes.ObjectivesTo conduct a systematic review and meta-analysis to elucidate the effects of increased BMI on fertility outcomes in females with no other comorbidities.Search strategyA comprehensive search was conducted using EMBASE, MEDLINE and the Cochrane library from January 2000 until July 2023.Data collection and analysisTwo authors independently conducted data extraction and assessed study quality. Odds ratio (OR) (dichotomous data), standardised mean difference (SMD) (continuous data) and 95% CIs were calculated.Main resultsNine eligible studies were identified: one natural conception and eight assisted reproductive technology (ART). Aggregated data revealed women with BMI ≥25 were less likely to attain clinical pregnancy (OR 0.76, 95% CIs 0.62 to 0.93, p=0.007), with BMI ≥30 associated with a further decreased likelihood of clinical pregnancy (OR 0.61, 95% CIs 0.39 to 0.98, p=0.04). Women with raised BMI required longer duration of stimulation (SMD=0.08, 95% CIs 0.00 to 0.16, p=0.04) and obtained reduced oocytes (SMD=−0.11, 95% CIs −0.18 to −0.04, p=0.002).ConclusionsThese data demonstrate an adverse impact of being overweight/obese on ART outcomes in women with no other diagnosed medical comorbidities and highlight the distinct lack of data concerning the effects of isolated obesity on natural conception. Infertility represents an enormous burden for couples and society; it is essential to identify and tackle modifiable risk factors to improve chances of conception.PROSPERO registration numberCRD42022293631.
Development and psychometric testing of a scale for diet self-management among urban residents in China: a cross-sectional study
Authors: Zhou Li , Wei Lai , Chu Yalin , Tang Yuhong 
Published: November 2024

Objective

Design
The diet self-management scale (DSE-MS) items were identified and evaluated by literature and guideline review, expert consultation and pilot testing. Factor structure was tested by randomly dividing the sample into two equal groups for exploratory factor analysis (EFA) and confirmatory factor analysis (CFA). The scale was further tested for internal consistency, convergent validity, discriminant validity and known-group validity.

Setting
A city in China.

Participants
A total of 724 urban residents from a city in China participated in this study in 2023.

Results
The final DSE-MS included 45 items and showed good internal consistency with a Cronbach’s alpha coefficient of 0.961. EFA identified 6 dimensions explaining 67.89% of the total variance: cognition (11 items), microenvironment (12 items), macroenvironment (4 items), safety management (7 items), nutrition management (6 items) and environment management (5 items). The CFA showed a good model fit of the six-dimension scale: χ2/df=1.8878, root mean square error of approximate=0.0496, Comparing Fit Index=0.9425, Incremental Fit Index=0.9428, Tucker-Lewis Index=0.9369 and standard root mean square residual=0.0525. Convergent validity was supported by high composite reliability (CR=0.89–0.96) and average variance extracted (AVE=0.58–0.72), while discriminant validity was confirmed by higher AVE estimates than the squared interconstruct correlations. The DSE-MS scores varied by various sample characteristics, verifying the known-group validity.

Conclusion
The 6-factor 45-item DSE-MS had good psychometric properties assessing diet self-management among urban citizens. The scale can guide future intervention programmes to improve diet self-management and evaluate the intervention effect. Further validation of the DSE-MS in other populations in other areas is needed to verify its wide application.
Association between sarcopenia index, intraoperative events and post-discharge mortality in patients undergoing percutaneous coronary intervention: a retrospective cohort study in a teaching hospital in Western China
Authors: Lu Shaochun , Huang Sha , Li Jianqun , Chen Xiaoyan , Zhao Lizhi 
Published: November 2024

ObjectivesTo examine the association between the sarcopenia index (SI) and the risk of intraprocedural events and post-discharge death during percutaneous coronary intervention (PCI).DesignA retrospective cohort study.SettingThe study was conducted at a teaching hospital in Western China.ParticipantsThe participants were patients aged 45 years and older who underwent PCI at the hospital and had an estimated glomerular filtration rate (eGFR) of ≥15 mL/min/1.73 m2. Patients who died during hospitalisation, as well as those with unknown death dates, those lost to follow-up and those with missing information for the SI calculation, were excluded.Primary and secondary outcome measuresThe SI was calculated as serum creatinine/cystatin C (Cr/CysC) × 100. The high-SI group was defined as the highest quartile, while the remaining participants were included in the low-SI group. Intraprocedural events included intraprocedural coronary slow flow (CSF)/coronary artery no-reflow (CNR) and malignant ventricular arrhythmia (MVA). In the event of death, the date of death was recorded.ResultsThe study included 497 patients who underwent PCI in our hospital, of whom 369 (74.25%) were males. A total of 57 (11.47%) patients developed CSF, 100 (20.12%) developed CNR and 4 (0.8%) developed MVA. Forty-four (8.85%) patients died post-discharge. The proportion of patients in the low-SI group who developed CSF was higher than those who did not (16.94% vs 9.65%, p=0.027). In addition, the average SI was lower in patients who developed CSF than in those who did not (81.99 vs 87.11, p=0.043). After adjusting for possible confounding factors, logistic regression analysis showed that the risk of CSF in the low-SI group was higher than that in the high-SI group (OR = 2.01, 95% CI: 1.04 to 3.89). In addition, it was found that the lower the SI, the higher the risk of CSF (OR = 0.983, 95% CI: 0.967 to 0.999).ConclusionsPatients with lower SI had a greater risk of developing CSF, and the lower the SI, the higher the risk of CSF. However, these data suggest that SI is not associated with CNR and the risk of post-discharge death in patients after PCI.
Use of dexmedetomidine during light versus deep anaesthesia on postoperative delirium among elderly patients undergoing major non-cardiac surgery: protocol for a multicentre randomised factorial trial
Authors: Shi Hai-Jing , Zhuang Min-Yuan , Hu Jing-Hui , Long Yu-Qin , Gao Yan-Ping , Zheng Zhong , Feng Xiao-Mei , Ji Fu-Hai , Peng Ke 
Published: November 2024

IntroductionElderly patients are at a high risk of postoperative delirium (POD), leading to increased postoperative morbidity and mortality. The use of dexmedetomidine and depth of anaesthesia may influence POD. This study aims to determine the effects of dexmedetomidine infusion versus normal saline placebo during light versus deep anaesthesia on POD among elderly patients undergoing major non-cardiac surgery.Methods and analysisThis prospective, multicentre, randomised, controlled, factorial trial will be conducted at three tertiary hospitals in Jiangsu, China. We will recruit a total of 420 patients who are at least 60 years old and undergoing major non-cardiac surgery (thoracic, abdominal, urology, orthopaedic and spine surgery) under general anaesthesia. Patients will be randomised (1:1:1:1) to receive one of four anaesthesia regimens: (1) dexmedetomidine and light anaesthesia, (2) dexmedetomidine and deep anaesthesia, (3) placebo and light anaesthesia or (4) placebo and deep anaesthesia. Dexmedetomidine will be infused at 0.5 µg/kg/h throughout surgery, and intraoperative bispectral index target will be 55 for light anaesthesia and 40 for deep anaesthesia. The primary outcome is the occurrence of POD during the first 7 days postoperatively or until hospital discharge, assessed using the 3-min Confusion Assessment Method two times per day. The secondary outcomes include days with POD, type of POD, pain scores at rest and on movement at 24 and 48 hours postoperatively, patient-controlled intravenous fentanyl consumption during 0–24 and 24–48 hours postoperatively, hypotension, bradycardia, postoperative nausea and vomiting, non-delirium complications, length of postoperative hospital stay, 30-day cognitive function and 30-day mortality. Data will be analysed on a modified intention-to-treat basis.Ethics and disseminationThis trial was approved by the Ethics Committee of the First Affiliated Hospital of Soochow University and each participating centre. The trial results will be published in a peer-reviewed journal.Trial registrationChinese Clinical Trial Registry (ChiCTR2300073271)