bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian sampling with BeAtlas, a grid of synthetic Be star spectra I. Recovering the fundamental parameters of α Eri and β CMi
Authors: Rubio A C , Carciofi A C , Ticiani P , Mota B C , Vieira R G , Faes D M , Genaro M , de Amorim T H , Klement R , Araya I , Arcos C , Curé M , Domiciano de Souza A , Georgy C , Jones C E , Suffak M W , Silva A C F 
Published: September 2023

ABSTRACT
Classical B emission (Be) stars are fast rotating, near-main-sequence B-type stars. The rotation and the presence of circumstellar discs profoundly modify the observables of active Be stars. Our goal is to infer stellar and disc parameters, as well as distance and interstellar extinction, using the currently most favoured physical models for these objects. We present BeAtlas, a grid of $61\, 600$ non-local thermodynamic equilibrium radiative transfer models for Be stars, calculated with the hdust code. The grid was coupled with a Monte Carlo Markov chain (MCMC) code to sample the posterior distribution. We test our method on two well-studied Be stars, α Eri and β CMi, using photometric, polarimetric, and spectroscopic data as input to the code. We recover literature determinations for most of the parameters of the targets, in particular the mass and age of α Eri, the disc parameters of β CMi, and their distances and inclinations. The main discrepancy is that we estimate lower rotational rates than previous works. We confirm previously detected signs of disc truncation in β CMi and note that its inner disc seems to have a flatter density slope than its outer disc. The correlations between the parameters are complex, further indicating that exploring the entire parameter space simultaneously is a more robust approach, statistically. The combination of BeAtlas and Bayesian-MCMC techniques proves successful, and a powerful new tool for the field: The fundamental parameters of any Be star can now be estimated in a matter of hours or days.
PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance
Authors: Yan Han , Hu Zhirui , Thomas Gregg W C , Edwards Scott V , Sackton Timothy B , Liu Jun S 
Published: September 2023

Abstract
An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here, we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations, and show that PhyloAcc-GT is a robust tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.
Choosing conservative care in advanced chronic kidney disease: a scoping review of patients’ perspectives
Authors: Jongejan Micha , de Lange Sanne , Bos Willem Jan W , Pieterse Arwen H , Konijn Wanda S , van Buren Marjolijn , Abrahams Alferso C , van Oevelen Mathijs 
Published: September 2023

ABSTRACT

Background
Conservative care (CC) is a viable treatment option for some patients with kidney failure. Choosing between dialysis and CC can be a complex decision in which involvement of patients is desirable. Gaining insight into the experiences and preferences of patients regarding this decision-making process is an important initial step to improve care. We aimed to identify what is known about the perspective of patients regarding decision-making when considering CC.

Methods
PubMed, EMBASE and Cochrane databases were systematically searched on 23 February 2023 for qualitative and quantitative studies on patient-reported experiences on decision-making about CC. Data were analysed thematically.

Results
Twenty articles were included. We identified three major themes: creating awareness about disease and treatment choice, decision support and motivation to choose CC. Patients were often not aware of the option to choose CC. Patients felt supported by their loved ones during the decision-making process, although they perceived they made the final decision to choose CC themselves. Some patients felt pressured by their healthcare professional to choose dialysis. Reported reasons to choose CC were maintaining quality of life, treatment burden of dialysis, cost and the desire not to be a burden to others. In general, patients were satisfied with their decision for CC.

Conclusions
By focussing on the perspective of patients, we identified a wide range of patient experiences and preferences regarding the decision-making process. These findings can help to improve the complex decision-making process between dialysis and CC and to provide patient-centred care.
Pathophysiology and targeted treatment of cholesterol crystal embolism and the related thrombotic angiopathy
Authors: Shi Chongxu , Mammadova‐Bach Elmina , Li Cong , Liu Dong , Anders Hans‐Joachim 
Published: September 2023

AbstractCholesterol crystal (CC) embolism is a complication of advanced atherosclerotic plaques located in the major arteries. This pathological condition is primarily induced by interventional and surgical procedures or occurs spontaneously. CC can induce a wide range of tissue injuries including CC embolism syndrome, a spontaneous or intervention‐induced complication of advanced atherosclerosis, while treatment of CC embolism has remained empiric. Vascular occlusions caused by CC embolism may exceed the ischemia tolerance of many tissues, particularly when small arteries are affected. The main approach to CC embolism is primary prophylaxis in patients at risk by stabilizing atherosclerotic plaques and avoiding unnecessary catheter interventions. During CC embolism, the use of platelet inhibitors to avoid abnormal activation and aggregation and anticoagulants may reduce the risk of vascular occlusions and tissue ischemia. This probably explains the relatively low prevalence of clinical manifestations of CC embolism, which are frequently found in autopsy studies. In this review, we summarized the current knowledge on the pathophysiology of CC embolism syndrome deriving from clinical observations and experimental mouse models. Furthermore, we described the risk factors of CC embolism in humans as well as the experimental studies based on empiric treatments. We also discuss potential therapeutic interventions based on recent experimental data and emerging drug options evolving from other research domains. Given the substantial unmet medical need to improve the outcomes of CC embolism, the identification of effective treatment strategies is urgently needed.
Hyperbaric Oxygen Therapy Inhibits Neuronal Ferroptosis After Spinal Cord Injury in Mice
Authors: Yao Ruizhang , Liu Mo , Liang Fang , Sun Zhencheng , Yang Jing , Zhou Junlin , Su Qingjun , Liu Xuehua 
Published: September 2023

Study Design.
Basic science study investigating the potential molecular mechanisms of hyperbaric oxygen (HBO) therapy in mice with spinal cord injury (SCI).

Objective.
We aimed to explore the intrinsic mechanisms of HBO for SCI through the lens of ferroptosis in the subacute phase.

Summary of Background Data.
HBO has been observed to facilitate the restoration of neurological function subsequent to SCI. Ferroptosis is a distinct cellular death mechanism that can be distinguished from apoptosis, necrosis, and autophagy. However, the precise relationship between these two phenomena remains poorly understood.

Methods.
We established an SCI model and employed a range of techniques, including behavioral assessments, electron microscopy, immunofluorescence, RT-qPCR, Western blotting (WB), Glutathione (GSH) measurement, and iron assay, to investigate various aspects of HBO therapy on SCI in mice. These included analyzing mitochondrial morphology, neuronal count, GSH levels, iron levels, and the expression of genes (Acyl-CoA synthetase family member-2, Iron-responsive element-binding protein-2) and proteins (Glutathione peroxidase 4; system Xc-light chain) associated with ferroptosis. The study included three groups: Sham-operated, SCI, and HBO. Group comparisons were performed using one-way analysis of variance and one-way repeated measures analysis of variance, followed by Tukey’s post hoc test. Statistical significance was set at a P < 0.05.

Results.
Our findings revealed that HBO therapy significantly enhanced the recovery of lower limb motor function in mice following SCI in the subacute phase. This was accompanied by upregulated expression of GPX4 and system Xc-light chain proteins, elevated GSH levels, increased number of NeuN+ cells, decreased expression of the iron-responsive element-binding protein-2 gene, and reduced iron concentration.

Conclusions.
Our research suggests that HBO therapy has the potential to be an effective treatment for SCI in the subacute phase by mitigating ferroptosis.
Molecular classification of small cell lung cancer subtypes: Characteristics, prognostic factors, and clinical translation
Authors: Guo Hanfei , Li Wenqian , Guo Ye , Chen Naifei , Cui Jiuwei 
Published: September 2023

Abstract
Small cell lung cancer (SCLC) is a highly malignant tumor with a very poor prognosis; therefore, more effective treatments are urgently needed for patients afflicted with the disease. In recent years, emerging molecular classifications based on key transcription factors of SCLC have provided more information on the tumor pathophysiology, metastasis, immune microenvironment, and acquired therapeutic resistance and reflected the intertumoral heterogeneity of the various SCLC phenotypes. Additionally, advances in genomics and single-cell sequencing analysis have further revealed the high intratumoral heterogeneity and plasticity of the disease. Herein, we review and summarize these recent lines of evidence and discuss the possible pathogenesis of SCLC.
Outcome Analysis of Combined Surgical Approaches in Advanced-stage Upper Extremity Breast Cancer-related Lymphedema
Authors: Myung Yujin , Park Joseph Kyu-hyung , Beom Jaewon , Lim Jae-Young , Park Young Suk , Ahn Sang-Hoon , Kang Eunyoung , Shin Hee-Chul , Kim Eun-Kyu , Nam Sun-Young , Heo Chan Yeong , Jeong Jae Hoon 
Published: September 2023

Background:
This study aimed to discuss several surgical approaches for advanced-stage breast cancer-related lymphedema and compared their treatment outcomes.

Methods:
The patients who underwent surgery with International Society of Lymphology stage III lymphedema were included in this study. The three surgical methods used here were (1) suction-assisted lipectomy with lymphovenous anastomosis, (2) autologous breast reconstruction with muscle-sparing transverse rectus abdominis muscle flap combined with inguinal lymph node transfer, and (3) vascularized lymph node transfer with free omental flap. Analysis of the postoperative outcomes in the patients was based on the difference in volume between patients pre- and postoperatively, LYMPH-Q questionnaire, and bioelectrical impedance analysis.

Results:
Eighty-seven patients with stage IIb or higher disease underwent surgery. 38 patients underwent suction-assisted lipectomy + lymphovenous anastomosis, 23 underwent autologous breast reconstruction with vascularized lymph node transfer + lymphovenous anastomosis, and 26 underwent right gastroepiploic omental vascularized lymph node transfer with lymphovenous anastomosis. The LYMPH-Q questionnaire, which evaluates patients’ subjective satisfaction, showed that the autologous breast reconstruction group showed the greatest improvement, whereas in bioimpedance analysis, the omental flap group demonstrated the greatest postoperative improvement compared with preoperative values. However, suction-assisted lipectomy was considered the most effective surgical method for reducing limb volume in patients with high-stage lymphedema accompanied by fibrosis and volume increase.

Conclusions:
We observed slightly different clinical effects for each surgical method; however, all surgical methods demonstrated a reduction in the degree of edema and an increase in patient satisfaction.
Modified L-shaped incision technique for supracardiac total anomalous pulmonary venous connection as an alternative to sutureless technique
Authors: Feng Zicong , He Qiyu , Yuan Jianhui , Dou Zheng , Wu Dongdong , Liu Yuze , Rui Lu , He Fengpu , Wu Zhongkai , Li Shoujun 
Published: September 2023

Background:
Modified L-shaped incision technique (MLIT) was successfully applied to the repair of supracardiac total anomalous pulmonary venous connection (TAPVC) with promising mid-term outcomes. It is, however, unclear whether or not MLIT could be an alternative to sutureless technique (ST).

Methods:
All patients (n=141) who underwent MLIT or ST repair for supracardiac TAPVC between June 2009 to June 2022 were included and a propensity score-matched analysis was performed to reduce the heterogeneity.

Results:
MLIT was performed in 80.9% (114/141), whereas ST was performed in 19.1% (27/141). Patients who underwent MLIT repair had a lower incidence of pulmonary veinous obstruction (PVO)-related reintervention (1.8% vs. 18.5%, P=0.002), and late mortality (2.6% vs. 18.2%, P=0.006). Overall survival at 10 years was 92.5% (87.7%-97.7%) for MLIT and 66.8% (44.4%-100%) for ST (P=0.012). Freedom from postoperative PVO at 10 years was 89.1% (83.2%-95.5%) for MLIT and 79.9% (65.6%-97.4%) for ST (P=0.12). Cox proportional hazards regression identified prolonged mechanical ventilation duration, postoperative PVO, respiratory dysfunction and low cardiac output syndrome were associated with postoperative death and PVO-related reintervention.

Conclusions:
The MLIT strategy is a safe, technologically feasible, and effective approach for supracardiac TAPVC, which is associated with more favourable and promising freedom from death and PVO-related reintervention.
Is Positive Communication Sufficient to Modulate Procedural Pain and Anxiety in the Emergency Department? A Randomized Controlled Trial
Authors: Berna Chantal , Favre-Bulle Anne , Bonzon Adélaïde , Gross Nathan , Gonthier Ariane , Gerhard-Donnet Hélène , Taffé Patrick , Hugli Olivier 
Published: September 2023

ABSTRACT

Objective
Research suggests that therapeutic communication could enhance patient comfort during medical procedures. Few studies have been conducted in clinical settings, with adequate blinding. Our hypothesis was that a positive message could lead to analgesia and anxiolysis, and that this effect would be enhanced by an empathetic interaction with the nurse performing the procedure, compared with an audio-taped message. This study aimed to modulate the contents and delivery vector of a message regarding peripheral intravenous catheter (PIC) placement in the emergency department (ED).

Methods
This study was a 2 + 2 randomized controlled trial registered on ClinicalTrials.gov (NCT03502655). A positive versus standard message was delivered through audio tape (double-blind) in the first phase (N = 131) and through the nurse placing the catheter (single-blind) in the second phase (N = 120).

Results
By design, low practitioner empathic behavior was observed in the first phase (median, 1 of 5 points). In the second phase, higher empathic behavior was observed in the positive than in the standard message (median, 2 versus 3, p < .001). Contrary to our hypothesis, the intervention did not affect pain or anxiety reports due to PIC placement in either phase (all p values > .2).

Conclusions
The positive communication intervention did not impact pain or anxiety reports after PIC. There might have been a floor effect, with low PIC pain ratings in a context of moderate pain due to the presenting condition. Hence, such a therapeutic communication intervention might not be sufficient to modulate a mild procedural pain in the ED.
Field study to determine the reliability of HIV viral load results shows minimal impact of delayed testing
Authors: Hardie Diana , Newman Howard , Ried Joanna , Hsiao Nei-Yuan , van Zyl Gert , Hans Lucia , Odayar Jasantha , Korsman Stephen 
Published: September 2023

AbstractUnderstanding factors that impact on the accuracy of HIV viral load (VL) results is key to quality improvements of VL programmes, particularly in resource limited settings. In this study we evaluated whether testing delay and room temperature storage (between 25-30°C) prior to testing affected results. 249 individuals who were on antiretroviral therapy, or with newly diagnosed HIV, were recruited and three PPT samples were collected from each patient. One sample was tested within 24 hours, while the others were stored un-centrifuged at ambient temperature prior to testing.Centrifugation and testing of matched samples were performed on days 4 and 7 after collection. In samples with initial VL >2 log copies/mL, time delay and ambient temperature storage had minimal impact. When grouped according to day 1 VL range, 96-100% of samples at day 4 and 93-100% at day 7 had a VL within 0.5 log copies/mL of the first result. Greatest variability was observed at day 4 and 7 when the day 1 VL was <2 log copies/mL, however, there was no trend of increasing difference with time. Of day 1 samples with undetectable VL or VL <50copies/mL, 80% and 78% had concordant results at days 4 and 7, respectively. Detection in later samples appeared to be stochastic, rather than showing a worsening trend. These results provide further evidence that VL is stable in PPT tubes for up to 7 days when stored at room temperature. It shows that there is significant variability in samples with VL close to the limit of detection, not affected by testing delay. Stochastic variation or technical factors that may increase the chance of false positive results could possibly account for this.
Integrated antigenic and nucleic acid detection in single virions and virion-infected host-derived extracellular vesicles
Authors: Nguyen Kim Truc , Rima Xilal Y. , Nguyen Luong T. H. , Wang Xinyu , Kwak Kwang Joo , Yoon Min Jin , Li Hong , Chiang Chi-Ling , Doon-Ralls Jacob , Scherler Kelsey , Fallen Shannon , Godfrey Stephanie L. , Wallick Julie A. , Magaña Setty M. , Palmer Andre F. , Lee Inyoul , Nunn Christopher C. , Reeves Kimberly M. , Kaplan Henry G. , Goldman Jason D. , Heath James R. , Wang Kai , Pancholi Preeti , Lee L. James , Reátegui Eduardo 
Published: September 2023

AbstractVirion-mediated outbreaks are imminent and despite rapid responses, they continue to cause adverse symptoms and death. Therefore, tunable, sensitive, high-throughput assays are needed to control future virion-mediated outbreaks. Herein, we developed a tunablein situassay to selectively sort virions and infected host-derived extracellular vesicles (IHD-EVs) and simultaneously detect antigens and nucleic acids at a single-particle resolution. The Biochip Antigen and RNA Assay (BARA) enhanced sensitivities, enabling the detection of virions in asymptomatic patients, genetic mutations in single virions, and the continued long-term expression of virion-RNA in the IHD-EVs of post-acute sequelae of COVID-19 patients. The BARA revealed highly accurate diagnoses by simultaneously detecting the spike glycoprotein and nucleocapsid-encoding RNA on single SARS-CoV-2 virions in saliva and nasopharyngeal swab samples. Altogether, the single-particle detection of antigens and virion-RNA provides a tunable framework for the diagnosis, monitoring, and mutation screening of current and future outbreaks.TeaserThe BARA enables antigenic and nucleic acid testing in single virions for unprecedented perspectives on viral diseases
Gender and Socio-Economic Status as moderators in the associations between Social Support Sources and Adolescents’ Mental and Behavioral Health Indicators
Authors: Bermejo-Martins E. , Torres-Sahli M. , Madsen K. Rich , Tabs-Damgraads M. , Nielsen L. , Meilstrup C.B. , Toftager M. , Santini Z. I. 
Published: September 2023

AbstractBackgroundExtensive research has established the intricate links between diverse social support sources and vital adolescent health indicators, such as mental wellbeing (MWB), problematic social media use (PSMU), and physical activity (PA). However, existing studies have not explored these interrelationships within a unified model or examined the moderating effects of gender and socio-economic status (SES).MethodsThis cross-sectional study employed a representative Danish sample of 2.034 adolescents, aged 13 and 15 years. A Multi-group Structural Equation Model (SEM) and covariance-based comparisons analysis utilized items from Multidimensional Scales of Perceived Social Support, The Warwick–Edinburgh Mental Well-being Scale, Social Media Disorder Scale, and measures of PA duration and frequency.ResultsThe associations between MWB-Teacher Support and MWB-Classmate Support were stronger in low SES adolescents than those with mid-high SES. Notably, the PSMU-Family Support negative association was more pronounced among girls, while PSMU-Friend Support’s negative relationship was stronger among boys. The PA-Family Support positive relationship was more robust in boys, while the PA-Teacher Support positive association was stronger among low-mid SES adolescents than those in high SES. The positive correlation between PA and MWB was stronger among boys and mid-low SES adolescents.ConclusionsStrategies designed to enhance family and school support, considering gender and SES, could effectively promote MWB and deter behavioural issues like PSMU and sedentary behaviours in adolescents.