bluuebunny/crossref_metadata_2025 huggingface dataset:
The surface mass density of the Milky Way: does the traditional KZ approach work in the context of new surveys?
Authors: Cheng Xinlun , Anguiano Borja , Majewski Steven R , Arras Phil
Published: October 2023

We revisit the classical KZ problem – determination of the vertical force and implied total mass density distribution of the Milky Way disc – for a wide range of Galactocentric radius and vertical height using chemically selected thin and thick disc samples based on Apache Point Observatory Galactic Evolution Experiment spectroscopy combined with the Gaia astrometry. We derived the velocity dispersion profiles in Galactic cylindrical coordinates, and solved the Jeans equation for the two samples separately. The result is surprising that the total surface mass density as a function of vertical height as derived for these two chemically distinguished populations is different. The discrepancies are larger in the inner compared to the outer Galaxy, with the density calculated from thick disc being larger, independent of the Galactic radius. Furthermore, while there is an overall good agreement between the total mass density derived for the thick disc population and the standard halo model for vertical heights larger than 1 kpc, close to the mid-plane the mass density observed using the thick disc population is larger than that predicted from the standard halo model. We explore various implications of these discrepancies, and speculate their sources, including problems associated with the assumed density laws, velocity dispersion profiles, and the Galactic rotation curve, potential non-equilibrium of the Galactic disc, or a failure of the Navarro-Frenk-White (NFW) dark matter halo profile for the Milky Way. We conclude that the growing detail in hand on the chemodynamical distributions of Milky Way stars challenges traditional analytical treatments of the KZ problem.
Towards an astronomical foundation model for stars with a transformer-based model
Authors: Leung Henry W , Bovy Jo
Published: October 2023

Rapid strides are currently being made in the field of artificial intelligence using transformer-based models like Large Language Models (LLMs). The potential of these methods for creating a single, large, versatile model in astronomy has not yet been explored. In this work, we propose a framework for data-driven astronomy that uses the same core techniques and architecture as used by LLMs. Using a variety of observations and labels of stars as an example, we build a transformer-based model and train it in a self-supervised manner with cross-survey data sets to perform a variety of inference tasks. In particular, we demonstrate that a single model can perform both discriminative and generative tasks even if the model was not trained or fine-tuned to do any specific task. For example, on the discriminative task of deriving stellar parameters from Gaia XP spectra, we achieve an accuracy of 47 K in Teff, 0.11 dex in log g, and 0.07 dex in [M/H], outperforming an expert XGBoost model in the same setting. But the same model can also generate XP spectra from stellar parameters, inpaint unobserved spectral regions, extract empirical stellar loci, and even determine the interstellar extinction curve. Our framework demonstrates that building and training a single foundation model without fine-tuning using data and parameters from multiple surveys to predict unmeasured observations and parameters is well within reach. Such ‘Large Astronomy Models’ trained on large quantities of observational data will play a large role in the analysis of current and future large surveys.
Stable accretion in young stars: the cases of EX Lupi and TW Hya
Authors: Sicilia-Aguilar A , Campbell-White J , Roccatagliata V , Desira J , Gregory S G , Scholz A , Fang M , Cruz-Saenz de Miera F , Kóspál Á , Matsumura S , Ábrahám P
Published: October 2023

We examine the long-term spectroscopic and photometric variability of EX Lupi and TW Hya, studying the presence of stable accretion and the role it plays in the observed variability. Analysing the velocity modulations of the emission lines with star-melt, we obtain information on the structure of the accretion columns and the disc–star connection. The emission-line radial velocities reveal that TW Hya, like EX Lupi, has a remarkably stable or slow-varying accretion column footprint, locked to the star for several years. The line-emitting regions are non-polar for both EX Lupi and TW Hya, and species with different energies differ in position. In contrast, the continuum emission as observed in the photometry is very variable and can be modelled by hotspot(s) that change over time in phase, shape, temperature, size, and location with respect to the emission-line region. The continuum emission region may not be limited to the stellar surface, especially during episodes of high accretion. The broad-line emission observed in EX Lupi during episodes of increased accretion reveals a further structure, which can be fitted by non-axisymmetric disc in Keplerian rotation inwards of the corotation radius. Since the radial velocity modulation due to accretion footprints is so stable, we used it to search for further velocity modulations. While no residual modulation (other than caused by stellar rotation) is found in these objects, a similar analysis could help to identify young planets/companions. Therefore, determining whether stable accretion footprints are common among young stars is a key to detect young planets.
Combing the brown dwarf desert with Gaia DR3
Authors: Stevenson Adam T , Haswell Carole A , Barnes John R , Barstow Joanna K
Published: October 2023

We have created an up-to-date catalogue of 214 brown dwarfs (BDs) in binaries with P < 104 d. This allows us to examine the population statistics of the BD desert. We searched Gaia third data release (DR3) non-single star (NSS) results for orbital inclinations of BD candidates, deriving 12 new masses. Three remain as desert BDs whereas nine candidates are found to be low-mass stars. We improved the radial velocity (RV) solutions for three previously studied BD candidates. A further 19 BD masses with periods less than ∼1200 d were identified in the DR3 binary_masses data base. We confirm a valley in the mass distribution with a minimum around 30–35 Mjup, and find that periods <100 d are still underpopulated in comparison with longer periods. The updated mass and eccentricity distribution of BDs still shows a marginally statistically significant split into high- and low-mass BD populations. This hints at two different parent distributions, and two potential origins – either akin to planetary formation, or stellar. There are no low-eccentricity BDs at periods around 100 d. The mass–metallicity distribution of BDs indicates that core accretion is not the dominant formation mechanism for BDs as they do not follow the same trends that giant exoplanets do with metallicity. We identify a diagonal envelope bounding the Gaia BDs in the mass–period plane due to the detection thresholds of the currently available NSS solutions from 34 months of data.
A photon burst clears the earliest dusty galaxies: modelling dust in high-redshift galaxies from ALMA to JWST
Authors: Tsuna Daichi , Nakazato Yurina , Hartwig Tilman
Published: October 2023

The generation and evolution of dust in galaxies are important tracers for star formation, and can characterize the rest-frame ultraviolet to infrared emission from the galaxies. In particular understanding dust in high-redshift galaxies are important for observational cosmology, as they would be necessary to extract information on star formation in the early Universe. We update the public semi-analytical model Ancient Stars and Local Observables by Tracing Halos (a-sloth) to model the evolution of dust, focusing on high-redshift star-forming galaxies with stellar masses of ∼108–1010 M⊙ observed by ALMA (z ≈ 7) and JWST (z ≈ 11). We find that these galaxies should qualitatively differ in their star formation properties; while the samples in ALMA are explained by dust growth in normal star-forming galaxies, the lack of dust in the samples by JWST requires dust ejection by radiation pressure due to recent highly efficient star formation within a few 10 Myr, with order 100 times higher efficiency than normal galaxies calibrated by a-sloth. Depending on where the JWST galaxies locate on the luminosity function, their bursty star formation histories inferred from our model can have impacts for rates of star formation, supernova explosion, stellar feedback, and detectability of dusty, mature galaxies in the very early Universe.
Computer image analysis with artificial intelligence: a practical introduction to convolutional neural networks for medical professionals
Authors: Kourounis Georgios , Elmahmudi Ali Ahmed , Thomson Brian , Hunter James , Ugail Hassan , Wilson Colin
Published: October 2023

Artificial intelligence tools, particularly convolutional neural networks (CNNs), are transforming healthcare by enhancing predictive, diagnostic, and decision-making capabilities. This review provides an accessible and practical explanation of CNNs for clinicians and highlights their relevance in medical image analysis. CNNs have shown themselves to be exceptionally useful in computer vision, a field that enables machines to ‘see’ and interpret visual data. Understanding how these models work can help clinicians leverage their full potential, especially as artificial intelligence continues to evolve and integrate into healthcare. CNNs have already demonstrated their efficacy in diverse medical fields, including radiology, histopathology, and medical photography. In radiology, CNNs have been used to automate the assessment of conditions such as pneumonia, pulmonary embolism, and rectal cancer. In histopathology, CNNs have been used to assess and classify colorectal polyps, gastric epithelial tumours, as well as assist in the assessment of multiple malignancies. In medical photography, CNNs have been used to assess retinal diseases and skin conditions, and to detect gastric and colorectal polyps during endoscopic procedures. In surgical laparoscopy, they may provide intraoperative assistance to surgeons, helping interpret surgical anatomy and demonstrate safe dissection zones. The integration of CNNs into medical image analysis promises to enhance diagnostic accuracy, streamline workflow efficiency, and expand access to expert-level image analysis, contributing to the ultimate goal of delivering further improvements in patient and healthcare outcomes.
N-terminal pro-brain natriuretic peptide is a biomarker for cardiovascular damage in systemic lupus erythematous: a cross-sectional study
Authors: Sacre Karim , Vinet Evelyne , Pineau Christian A , Mendel Arielle , Kalache Fares , Grenier Louis-Pierre , Huynh Thao , Bernatsky Sasha
Published: October 2023

Objectives

Prediction models based on traditional risk factors underestimate cardiovascular (CV) risk in systemic lupus erythematosus (SLE). In a large sample of unselected SLE patients, we investigated cross-sectional associations of NT-proBNP with cardiovascular damage (CVD).

Methods

Serum NT-proBNP was measured in SLE patients enrolled in the MUHC Lupus Clinic registry. Serum was collected between March 2022 and April 2023 at annual research visits. The primary outcome was CVD identified on the SLICC Damage Index. Factors associated with CVD and NT-proBNP levels were determined.

Results

Overall, 270 SLE patients [female 91%, median age 50.7 (first quartile to third quartile: 39.6–62.1) years] were analysed for the primary outcome. Among them, 33 (12%) had CVD. The ROC curve for NT-proBNP demonstrated strong associations with CVD (AUC 0.78, 95% CI 0.69–0.87) with a threshold of 133 pg/ml providing the best discrimination for those with/without CVD. Hypertension (OR 3.3, 95% CI 1.2–9.0), dyslipidaemia (OR 3.6, 95% CI 1.3–9.6) and NT-proBNP >133 pg/ml (OR 7.0, 95% CI, 2.6–19.1) were associated with CVD in the multivariable logistic regression model. Increased NT-proBNP levels were associated with age (OR 4.2, 95% CI 2.2–8.3), ever smoking (OR 1.9, 95% CI 1.0–3.5), reduced eGFR (4.1, 95% CI 1.3–13.1), prior pericarditis/pleuritis (OR 2.5, 95% CI 1.4–4.5) and aPL antibodies (OR 2.6, 95% CI 1.4–4.9).

Conclusion

NT-proBNP is a biomarker for CV damage in SLE. The novel associations of NT-proBNP levels with prior pericarditis/pleuritis and aPL antibodies suggest new avenues for research to better understand what drives CV risk in SLE.
Impact of Social Determinants of Health on Adolescent Idiopathic Scoliosis Curve Severity
Authors: Orellana Kevin J. , Lee Julianna , Yang Daniel , Hauth Lucas , Flynn John M.
Published: October 2023

Introduction:

Social determinants of health have been shown to influence the health and outcomes of pediatric patients. Adolescent idiopathic scoliosis (AIS) may be particularly sensitive to such factors as early diagnosis and treatment can obviate the need for surgical intervention. The purpose of this study was to analyze the effect that social determinants of health have on the severity of AIS at presentation and at the time of surgery.

Methods:

A retrospective review was conducted for consecutive patients who underwent posterior spinal fusion for AIS from 2020 to 2022. Demographic data was collected, while insurance status (private vs. public) and childhood opportunity index (COI) categories (LOW vs. HIGH) were used as a proxy for socioeconomic status. Curve magnitude at the initial presentation and at the latest preoperative visit were recorded with a threshold of 25 to 40 degrees considered within the bracing range. Univariate and multivariate analysis was done to compare differences between subgroups as appropriate.

Results:

A total of 180 patients with mean initial and preoperative major curve angles of 48 and 60 degrees were included. Statistically significant differences in race and insurance types were appreciated, with the LOW COI group having a higher proportion of underrepresented minority and publicly insured patients than the HIGH COI group (P<0.001). Patients within the LOW COI group presented with an initial curve that was, on average, 6 degrees more severe than those within the HIGH group (P=0.009) and a preoperative curve that was 4 degrees larger than those within the HIGH group (P=0.015). Similarly, only 13% of patients within the LOW COI group presented with curves within the bracing threshold, compared with 31% in the HIGH COI group (P=0.009).

Conclusion:

Socioeconomic status plays a significant role in the severity of AIS. Specifically, patients with lower COI tend to present with curve magnitudes beyond what is responsive to nonsurgical treatment, leading to larger curves at the time of surgery. Future work should focus on addressing social inequalities to optimize the treatment and outcomes of AIS patients.

Level of Evidence:

Level III- Retrospective Comparative Study.
Pharmacist Avoidance or Reductions in Medical Costs in Critically and Emergently Ill Pediatrics: PHARM-PEDS Study
Authors: Kiskaddon Amy L. , Smith Michelle M. , Gilliland Frankie , Rech Megan A. ,   Pharmacist Avoidance or Reductions in Medical Costs in Critically and Emergently Ill Pediatrics (PHARM-PEDS) Investigators
Published: October 2023

OBJECTIVES:

To comprehensively classify interventions performed by pediatric critical care clinical pharmacists and quantify cost avoidance (CA) generated through their accepted interventions.

DESIGN:

A multicenter, prospective, observational study performed between August 2018 and January 2019.

SETTING:

Academic and community hospitals in the United States with pediatric critical care units.

SUBJECTS:

Pediatric clinical pharmacists.

INTERVENTIONS:

Pharmacist recommendations were classified into one of 38 total intervention categories associated with CA.

MEASUREMENTS AND MAIN RESULTS:

Nineteen pediatric pharmacists at five centers documented 1,458 accepted interventions during 112 shifts on 861 critically ill pediatric patients. This calculated to an associated CA of $450,590. The accepted interventions and associated CA in the six established categories included as follows: adverse drug event prevention (155 interventions, $118,901 CA), resource utilization (267 interventions; $59,020), individualization of patient care (898 interventions, $217,949 CA), prophylaxis (8 interventions, $453 CA), hands-on care (30 interventions, $35,509 CA), and administrative/supportive tasks (108 interventions, $18,758 CA). The average associated CA was $309 per accepted intervention, $523 per patient day, and $4,023.13 per pediatric clinical pharmacist shift. The calculated potential annualized CA of accepted interventions from a pediatric pharmacist was $965,550, resulting in a potential monetary-associated CA-to-pharmacist salary ratio between $1.5:1 and $5.2:1.

CONCLUSIONS:

There is potential for significant avoidance of healthcare costs when pediatric pharmacists are involved in the care of critically and emergently ill pediatric patients, with a monetary potential CA-to-pediatric pharmacist salary ratio to be between $1.5:1 and $5.2:1.
Relationship of blood pressure measured in the calf with arm blood pressure and arterial stiffness: a general population study
Authors: Marques Edmilson R. , Bernardino Alana C. , Alvim Rafael O. , Schreiber Roberto , Krieger José Eduardo , Matos-Souza José R. , Sposito Andrei C. , Pereira Alexandre C. , Nadruz Wilson
Published: October 2023

Aim:

Leg blood pressure (BP) measurement is needed when arm BP evaluation is not feasible, and calf BP, especially when measured in standing position, may have greater association with cardiovascular remodeling than arm BP. This study evaluated the relationship between calf and arm BP, and investigated whether calf BP would be superior to arm BP in predicting increased arterial stiffness [pulse wave velocity (PWV) > 10 m/s].

Methods:

We evaluated clinical and laboratory characteristics, BP measurements, and PWV in 1397 individuals resident in Baependi, Brazil, between 2017 and 2019. Arm BP was measured in the seated and supine positions while calf BP was measured in supine and standing positions using digital oscillometric devices. Carotid–femoral PWV was measured using a noninvasive mechanotransducer.

Results:

The sample had 62.7% females, age = 48.1 ± 15.4 years and 8.4% with PWV >10 m/s. Results of linear regression analysis showed that BP values of 140/90 mmHg measured in the arm in supine and seated position were equivalent to calf supine BP values of 164/81 mmHg and 166/78 mmHg and calf standing BP values of 217/137 mmHg and 221/137 mmHg, respectively. Calf-arm BP differences were associated with age, glomerular filtration rate, body mass index, smoking, low-density lipoprotein-cholesterol, diabetes and height. Furthermore, stepwise logistic regression analysis revealed that arm supine systolic BP, but not calf BP measurements, was independently associated with increased arterial stiffness.

Conclusion:

Thresholds of ≈165/80 mmHg and ≈220/135 mmHg could be used for diagnosing hypertension when only calf measurements in supine and standing positions, respectively, are available. Conversely, calf BP was not superior to arm BP in predicting increased arterial stiffness.
Vascular Reconstruction After Cannulation for Support With Extracorporeal Membrane Oxygenation: Literature Review of Data in the Pediatric Population*
Authors: Zens Tiffany , Eldredge R. Scott , Gill Manrit , Mathew Steven , Molitor Mark
Published: October 2023

OBJECTIVES:

Extracorporeal membrane oxygenation (ECMO) is an invaluable life-support resource in the treatment of critically ill children. Traditionally, neck vascular cannulation requires ligation of the carotid artery and jugular vein. In this literature review, we identify rates of postoperative vessel patency, complications, and neurologic outcomes after vascular reconstruction following decannulation.

DATA SOURCES:

Embase, PubMed, and Cochrane Review.

STUDY SELECTION:

No publication date limits. Inclusion criteria comprised of studies addressing repair of the carotid artery and jugular vein after ECMO decannulation and outcomes from this procedure.

DATA EXTRACTION:

Authors identified publications on vascular reconstruction after ECMO decannulation, including possible technical considerations, complications, and outcomes.

DATA SYNTHESIS:

We identified 18 articles: 13 studies were limited to the neonatal population. The largest series included 51 patients after vascular reconstruction. The rate of postoperative arterial occlusion ranged from 11.8% to 17.8%, and overall patency rate postoperatively was 78.6%. No major thromboembolic events were reported. One study demonstrated an increase in neuroimaging abnormalities for patients undergoing ligation compared with vascular reconstruction. No studies demonstrated differences in functional neurodevelopmental testing.

CONCLUSIONS:

Vascular reconstruction after ECMO decannulation has been reported since 1990. Although reconstruction does not appear to carry significant short-term morbidity, there are no large prospective studies or randomized controlled trials demonstrating its efficacy in improving neurologic outcomes in ECMO patients. There is also a paucity of data regarding outcomes in older children or long-term ramifications of vascular reconstruction.
Evolution of Response-Based Radiotherapy for Hepatocellular Cancer
Authors: Elaimy Ameer L. , Cao Yue , Lawrence Theodore S.
Published: October 2023

Stereotactic body radiation therapy has emerged as a safe and effective treatment modality for properly selected hepatocellular cancer (HCC) patients with normal liver function. However, many HCC patients have reduced baseline liver function due to underlying cirrhosis or prior liver-directed therapies. Therefore, because of the increased risk of hepatotoxicity, the use of stereotactic body radiation therapy for patients with reduced liver function has been approached with caution. Individualized, response-based radiotherapy incorporates models, imaging tools, and biomarkers that determine the dose-response relationship of the liver before, during, and after treatment and has been useful in reducing the likelihood of liver damage without sacrificing tumor control. This review discusses the evolution of response-based radiotherapy for HCC and highlights areas for further investigation.
Acute Appendicitis Complicated by Septic Thrombophlebitis of the Portal Vein Shown by 18F-FDG and 68Ga-FAPI-46 PET/CT
Authors: Cai Jiayu , Xu Weizhi , Meng Tinghua , Pang YiZhen , Chen Haojun
Published: October 2023

Septic thrombophlebitis of the portal vein is a serious infectious disorder and is difficult to be diagnosed at an early stage. In this case, we presented 18F-FDG and 68Ga-FAPI-46 PET/CT findings in a 45-year-old man with acute appendicitis complicated by septic thrombophlebitis of the portal vein. 68Ga-FAPI-46 PET/CT showed intense radiotracer uptake in the thrombosis of the portal vein, with higher SUVmax and larger disease extent than 18F-FDG PET/CT. This case demonstrated that 68Ga-FAPI PET/CT may be a useful imaging modality for the diagnosis of this infectious condition.
Small Bowel Metastases From Malignant Phyllodes Breast Tumor Detected by 18F-FDG PET/CT
Authors: Yuan Meng , Han Bing , Zhang Nan , Lu Lu , Liu Shuai
Published: October 2023

The most common sites of distant metastases are lung, bone, pleura, and mediastinum in malignant phyllodes breast tumors. However, small bowel metastasis from malignant phyllodes breast tumors is rare. We reported that using CT and FDG PET/CT imaging we identified a case with small bowel metastasis from breast cancer. PET/CT scan showed that high 18F-FDG uptake occurred in the duodenum and jejunum. Histopathology and immunohistochemistry analyses further confirmed that malignant phyllodes tumors are derived from the breast.
A False-Positive Bone Oligometastatic Prostate Cancer in 18F-Choline PET/CT
Authors: Pretet Valentin , Moreau Aurélie , Larrouquere Louis , Mognetti Thomas , Kryza David
Published: October 2023

We report the case of a 71-year-old man undergoing initial assessment for a high-risk group prostate adenocarcinoma. His medical history includes gastric carcinoma treated with surgery and chemotherapy. 18F-choline PET/CT was performed for initial staging and displayed several intense foci uptake of sternum and thoracic vertebrae, suggestive of bone metastasis. Because of a chronic right jugulosubclavian confluent thrombosis related to his implantable chamber, a control was performed 3 weeks later. It showed spontaneous disappearance of those uptakes, consistent with pitfalls related to the collateral circulation induced by the chronic right subclavian vein thrombosis, despite the chronic anticoagulation.
A Novel Approach to Brain Tumor Classification Using Deep Neural Networks
Authors: Tummala Rohan
Published: October 2023

The American Cancer Society estimates that in 2023 about 24,810 malignant brain and spinal cord tumors will be diagnosed in the United States and about 18,990 people will die from these tumors. Early detection of malignant brain tumors is crucial in improving survival. Currently, MRI is the standard radiological method used to identify brain tumors. However, these tests are prone for human error, inefficiencies, and often require invasive tissue diagnosis for confirmation. Advancement in machine learning algorithms has shown to improve accuracy in detection of brain tumors. In this study, a novel deep learning approach, called Inception Resnet, a type of pretrained Convolutional Neural Network(CNN), was used to identify and classify three common brain tumors. These classes were pituitary, meningioma, and glioma. Pituitary tumors are the most harmless of the three as they are noncancerous. This contrasts with both glioma and high grade meningioma tumors which are life-threatening. It should be noted, however, that high grade meningioma tumors are very rare. Along with these three classes, a separate control class with no brain tumors was also used. This dataset contained 5,952 MRI images that included 1621 glioma images, 574 meningioma images, 1751 pituitary images and 2000 images with no tumor. Based on this data, a model was created that was able to diagnose brain tumors with an accuracy of 96.7%.
The MAGMA pipeline for comprehensive genomic analyses of clinicalMycobacterium tuberculosissamples
Authors: Heupink Tim H. , Verboven Lennert , Sharma Abhinav , Rennie Vincent , de Diego Fuertes Miguel , Warren Robin M. , Rie Annelies Van
Published: October 2023

Background

Whole genome sequencing (WGS) holds great potential for the management and control of tuberculosis. Accurate analysis of samples with low mycobacterial burden, which are characterized by low (<20x) coverage and high (>40%) levels of contamination, is challenging. We created the MAGMA (Maximum Accessible Genome forMtbAnalysis) bioinformatics pipeline for analysis of clinicalMtbsamples.

Methods and results

High accuracy variant calling is achieved by using a long seedlength during read mapping to filter out contaminants, variant quality score recalibration with machine learning to identify genuine genomic variants, and joint variant calling for lowMtbcoverage genomes. MAGMA automatically generates a standardized and comprehensive output of drug resistance information and resistance classification based on the WHO catalogue ofMtbmutations. MAGMA automatically generates phylogenetic trees with drug resistance annotations and trees that visualize the presence of clusters. Drug resistance and phylogeny outputs from sequencing data of 79 primary liquid cultures were compared between the MAGMA and MTBseq pipelines. The MTBseq pipeline reported only a proportion of the variants in candidate drug resistance genes that were reported by MAGMA. Notable differences were in structural variants, variants in highly conservedrrsandrrlgenes, and variants in candidate resistance genes for bedaquiline, clofazmine, and delamanid. Phylogeny results were similar between pipelines but only MAGMA visualized clusters.

Conclusion

The MAGMA pipeline could facilitate the integration of WGS into clinical care as it generates clinically relevant data on drug resistance and phylogeny in an automated, standardized, and reproducible manner.

Key points

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Accurate analysis of clinical samples is challenging when samples have high levels of contamination and lowMycobacterium tuberculosisgenome coverage

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When analyzing primary liquid (MGIT) cultures, the MAGMA pipeline generates clinically relevant drug resistance information (including major, minor and structural variants) and phylogeny in an automated, standardized and reproducible way.

-

MAGMA-generated phylogenetic trees are annotated with drug resistance information and updated with every run so that they can be used to make clinical or public health decisions

-

MAGMA reports drug resistance variants for all tier 1 and tier 2 candidate drug resistance conferring genes, with interpretation of their relevance to drug resistance (associated with drug resistance, not associated with drug resistance or unknown significance) based on the WHO catalogue of mutations inMycobacterium tuberculosis.
Automatic sleep stage classification using physiological signals acquired by Dreem headband
Authors: Dogaheh Shahla Bakian , Moradi Mohammad Hassan
Published: October 2023

In this paper, we aim to propose a model for automatic sleep stage classification based on physiological signals acquired by Dreem Headband and extreme gradient boosting (XGBoost) method. The dataset used in this study belongs to a challenge competition, namely as “Challenge Data”, held in 2017-2018, and is publicly available on their website. Recordings, includes 4 EEG channels (FpZ-O1, FpZ-O2, FpZ-F7, F8-F7), 2 Pulse oximeter (RED & infra-red), and 3 accelerometer channels (X, Y, Z). In this work, sleep stages have been scored according to the AASM standard. Different features were extracted from the physiological signals after applying a preprocessing step. Each of the elicited features from EEG and PPG signals is falling into one of the three categories: time-domain, frequency domain, or non-linear features. Moreover, ancillary features including body movement, frequency features, breathing frequency, and respiration rate variability were also extracted from the accelerometer signal. Significance of the extracted features was examined through the Kruskal Wallis test, and features with P-value>0.01 were discarded from features set. Finally, significant features were classified by using support vector machine (SVM), K-nearest neighbors (KNN), random forest (RF), and XGBoost classifiers. Due to the class imbalance problem, repeated stratified 5-fold cross-validation was performed in order to tune systems parameters. Results show that among the four above-mentioned models, XGBoost has the best performance for the 5-class classification problem with accuracy: 81.34%±0.76% and Kappa 0.7388±0.0101. The proposed model shows promising results, therefore the model can be implemented in Dreem headband to differentiate between sleep states efficiently and be applicable in clinical trial.
Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
Authors: Gerdes Patricia , Chan Dorothy , Lundberg Mischa , Sanchez-Luque Francisco J. , Bodea Gabriela O. , Ewing Adam D. , Faulkner Geoffrey J. , Richardson Sandra R.
Published: October 2023

Mice harbor ∼2800 intact copies of the retrotransposon Long Interspersed Element 1 (L1). The in vivo retrotransposition capacity of an L1 copy is defined by both its sequence integrity and epigenetic status, including DNA methylation of the monomeric units constituting young mouse L1 promoters. Locus-specific L1 methylation dynamics during development may therefore elucidate and explain spatiotemporal niches of endogenous retrotransposition but remain unresolved. Here, we interrogate the retrotransposition efficiency and epigenetic fate of source (donor) L1s, identified as mobile in vivo. We show that promoter monomer loss consistently attenuates the relative retrotransposition potential of their offspring (daughter) L1 insertions. We also observe that most donor/daughter L1 pairs are efficiently methylated upon differentiation in vivo and in vitro. We use Oxford Nanopore Technologies (ONT) long-read sequencing to resolve L1 methylation genome-wide and at individual L1 loci, revealing a distinctive “smile” pattern in methylation levels across the L1 promoter region. Using Pacific Biosciences (PacBio) SMRT sequencing of L1 5′ RACE products, we then examine DNA methylation dynamics at the mouse L1 promoter in parallel with transcription start site (TSS) distribution at locus-specific resolution. Together, our results offer a novel perspective on the interplay between epigenetic repression, L1 evolution, and genome stability.
Multi-stage skewed grey cloud clustering model and its application
Authors: Yang Jie , Zhang Manman , Shangguan Linjian , Shi Jinfa
Published: October 2023

Purpose

The possibility function-based grey clustering model has evolved into a complete approach for dealing with uncertainty evaluation problems. Existing models still have problems with the choice dilemma of the maximum criteria and instances when the possibility function may not accurately capture the data's randomness. This study aims to propose a multi-stage skewed grey cloud clustering model that blends grey and randomness to overcome these problems.

Design/methodology/approach

First, the skewed grey cloud possibility (SGCP) function is defined, and its digital characteristics demonstrate that a normal cloud is a particular instance of a skewed cloud. Second, the border of the decision paradox of the maximum criterion is established. Third, using the skewed grey cloud kernel weight (SGCKW) transformation as a tool, the multi-stage skewed grey cloud clustering coefficient (SGCCC) vector is calculated and research items are clustered according to this multi-stage SGCCC vector with overall features. Finally, the multi-stage skewed grey cloud clustering model's solution steps are then provided.

Findings

The results of applying the model to the assessment of college students' capacity for innovation and entrepreneurship revealed that, in comparison to the traditional grey clustering model and the two-stage grey cloud clustering evaluation model, the proposed model's clustering results have higher identification and stability, which partially resolves the decision paradox of the maximum criterion.

Originality/value

Compared with current models, the proposed model in this study can dynamically depict the clustering process through multi-stage clustering, ensuring the stability and integrity of the clustering results and advancing grey system theory.
The relationship between service quality of banking kiosk and customer satisfaction: the moderating role of technology readiness
Authors: Nguyen Hong Quan , Nguyen Quynh Huong , Tran Phuong Thao , Trinh Ngoc Linh , Nguyen Quynh Trang
Published: October 2023

Purpose

The aim of this empirical study is to investigate an integrated model that captures the way service quality of banking kiosks (BK-SQ) exerts its impacts on customer perceived value and customer satisfaction and the moderating mechanism of technology readiness (TR) in the quality–satisfaction relationship in the banking sector in Vietnam.

Design/methodology/approach

An offline survey was conducted to obtain responses from 604 users of banking kiosks in Vietnam. Exploratory factor analysis, confirmatory factor analysis and structural equation modeling were used for data analysis. The moderating effect of TR was examined following the product indicator method.

Findings

The results validate significant positive correlations between BK-SQ, customer perceived value and customer satisfaction. Among six service quality dimensions, convenience is the most significant factor in predicting perceived service quality. The study also delineates how TR can moderate the link between service quality and customer satisfaction.

Research limitations/implications

Future studies may make further attempts to incorporate other human and demographic factors as a moderator into the research model.

Practical implications

Bank managers should strive to improve the operations of banking kiosks based on six aspects and increase TR levels of customers to boost customer satisfaction with banking kiosks.

Originality/value

The study contributes to the literature on service quality and self-service technologies (SSTs) by offering critical insights into how banks can make use of influence mechanisms in the model to enhance service quality and customer satisfaction.
Examining the role of heritage-destination attributes on travel constraints and revisit intention using multilevel analysis
Authors: Dabphet Siripen
Published: October 2023

Purpose

This study aimed to explore how the attributes of heritage destinations become constraints on tourists' intention to revisit these destinations and to provide stakeholders with strategies to mitigate travel constraints, thereby increasing tourists' revisit intention.

Design/methodology/approach

A quantitative research approach was used, and data collection utilised a convenience sampling method. A total of 1,250 tourists completed self-administered, on-site surveys. To analyse the collected data effectively and to test hypotheses, multilevel analysis models were created.

Findings

Heritage-destination attributes are found to mediate the impact of perceived constraints on tourists' intention to revisit heritage destinations. Positive perceptions of heritage and cultural attractions among tourists can mitigate the adverse effects of constraints on their intentions.

Research limitations/implications

This study only focused on examining the downward cross-level impact, i.e. from the macro level to the individual level. This could be beneficial for exploring an upward cross-level impact.

Practical implications

The findings provide strategic guidance for marketing programs to enhance the reputation of heritage destinations. By identifying and establishing attributes specific to heritage destinations that visitors perceive as the most appealing, program designers can effectively target their efforts. Additionally, the findings help stakeholders of heritage destinations develop and provide suitable heritage and cultural attractions and tourism infrastructure in line with tourists' preferences.

Originality/value

This study employed a multilevel approach to examine how heritage-destination attributes and related constraints on travelling on impact individuals' intentions to revisit destinations. The study considered a macro-based perspective to analyse these effects.
Value network partners' perception of co-creation and its impact on their satisfaction
Authors: Sambyal Rachita , Rishi Bikramjit , Mavi Anupreet Kaur , Marwaha Amandeep Singh
Published: October 2023

Purpose

Co-creating with value network partners (VNPs) in the tourism industry has become essential for delivering improved service quality and enhancing consumer experience. This research examines the impact of value co-creation on the satisfaction of VNPs. Further, the study examines the moderating effects of socio-demographic factors on the relation between co-creation and VNP satisfaction.

Design/methodology/approach

The study collected data from VNPs engaged in tourism-related activities (N = 392). It analysed the data through structural equation modelling using SPSS 20 and AMOS 21. The study used the stimulus-organism-response framework to understand VNP's perceptions regarding co-creation.

Findings

The results indicate a significant relationship between the value processes and networks, service offerings, conversations and dialogues and value proposition in relation to co-creation. Additionally, the study identifies the significance of age, education level, job experience and job nature. The findings of the study can enable tourism managers to formulate effective co-creation strategies.

Practical implications

The insights from the study enable tourism managers to devise co-creation strategies that nurture collaboration with VNPs. Managers can gain insights into the antecedents of the co-creation and the role of demographic factors in shaping strategies.

Originality/value

The study's findings have the potential to shape co-creation policies in the tourism and hospitality industry. Network partners and tourism companies can leverage insights from the study to develop and refine their co-creation policies. By bridging the gaps in the existing literature on value co-creation with network partners, the study contributes significantly to tourism and hospitality literature.
Linking positive psychology with reciprocal action learning
Authors: Lyons Paul
Published: October 2023

Purpose

The purpose of this paper, intended primarily for practitioners, is to demonstrate how features of psychological capital (PsyCap) may be combined with manager efforts to collaborate with an employee on an action learning project. In reciprocal action learning, manager and employee create a partnership to learn, achieve work-focused goals and advance their relationship. Initiatives aimed at positively stimulating employee assets and psychological or behavioral attributes can overlay the action learning process.

Design/methodology/approach

A narrative synthesis was used to examine three sources of empirical research from organizational psychology and human resource management: reciprocity, action learning and PsyCap. Information was integrated to create a guide, a model for managers for use in considering options about how to structure employee and self-learning, as well as options for use in stimulating employee assets and PsyCap.

Findings

The approach presented may serve as a practical guide for manager consideration. Research identifies several types of behaviors and activities intended to positively stimulate and reinforce the learning of both participants. The literature on PsyCap offers many initiatives for a manager to consider in assisting an employee to develop talent and positive attitudes. Such efforts have to be carefully tailored to the individual employee, the tasks at hand and the manager’s own learning needs.

Originality/value

The value of action learning is supported by a relatively large research base. The significance of PsyCap also has substantial support. Innovatively, this paper offers guidance to a manager in consideration of combining the attributes of both concepts to maximize positive effects on learning, personal growth, skill development and work achievement.
Practitioner warmth and empathy attenuates the nocebo effect and enhances the placebo effect
Authors: Barnes Kirsten , Wang Rachelle , Faasse Kate
Published: October 2023

Augmented patient–practitioner interactions that enhance therapeutic alliance can increase the placebo effect to sham treatment. Little is known, however, about the effect of these interactions on maladaptive health outcomes (i.e., the nocebo effect). Healthy participants (N = 84) were randomised to a 3‐day course of Oxytocin nasal drops (actually, sham treatment) in conjunction with a high‐warmth interaction (Oxy‐HW: N = 28), a low‐warmth interaction (Oxy‐LW: N = 28) or to a no treatment control group (NT: N = 28). All participants were informed that the Oxytocin treatment could increase psychological well‐being but was associated with several potential side effects. Treatment‐related side effects, unwarned symptoms, and psychological well‐being were measured at baseline and all post‐treatment days. Side effect reporting was increased in the Oxy‐LW condition compared to the other groups across all days. Conversely, increased psychological well‐being was observed in the Oxy‐HW condition, relative to the other conditions, but only on Day 1. Among those receiving treatment, positive and negative expectations, and treatment‐related worry, did not vary by interaction‐style, while psychological well‐being and side effect reporting were inversely associated at the level of the individual. Results have important implications for practice, suggesting poorer quality interactions may not only reduce beneficial health outcomes but also exacerbate those that are maladaptive.
Evaluation of the reproducibility of responses to nasal allergen challenge and effects of inhaled nasal corticosteroids
Authors: Bauer Rebecca N. , Xie Yanqing , Beaudin Suzanne , Wiltshire Lesley , Wattie Jennifer , Muñoz Caroline , Alsaji Nadia , Oliveria John Paul , Ju Xiaotian , MacLean Jonathan , Sommer Doron D. , Keith Paul K. , Satia Imran , Cusack Ruth P. , O'Byrne Paul M. , Sperinde Gizette , Hokom Martha , Li Olga , Banerjee Prajna , Chen Chen , Staton Tracy , Sehmi Roma , Gauvreau Gail M.
Published: October 2023

Background

Similar immune responses in the nasal and bronchial mucosa implies that nasal allergen challenge (NAC) is a suitable early phase experimental model for drug development targeting allergic rhinitis (AR) and asthma. We assessed NAC reproducibility and the effects of intranasal corticosteroids (INCS) on symptoms, physiology, and inflammatory mediators.

Methods

20 participants with mild atopic asthma and AR underwent three single blinded nasal challenges each separated by three weeks (NCT03431961). Cohort A (n = 10) underwent a control saline challenge, followed by two allergen challenges. Cohort B (n = 10) underwent a NAC with no treatment intervention, followed by NAC with 14 days pre‐treatment with saline nasal spray (placebo), then NAC with 14 days pre‐treatment with INCS (220 μg triamcinolone acetonide twice daily). Nasosorption, nasal lavage, blood samples, forced expiratory volume 1 (FEV1), total nasal symptom score (TNSS), peak nasal inspiratory flow (PNIF) were collected up to 24 h after NAC. Total and active tryptase were measured as early‐phase allergy biomarkers (≤30 min) and IL‐13 and eosinophil cell counts as late‐phase allergy biomarkers (3–7 h) in serum and nasal samples. Period‐period reproducibility was assessed by intraclass correlation coefficients (ICC), and sample size estimates were performed using effect sizes measured after INCS.

Results

NAC significantly induced acute increases in nasosorption tryptase and TNSS and reduced PNIF, and induced late increases in nasosorption IL‐13 with sustained reductions in PNIF. Reproducibility across NACs varied for symptoms and biomarkers, with total tryptase 5 min post NAC having the highest reproducibility (ICC = 0.91). Treatment with INCS inhibited NAC‐induced IL‐13 while blunting changes in TNSS and PNIF. For a similar crossover study, 7 participants per treatment arm are needed to detect treatment effects comparable to INCS for TNSS.

Conclusion

NAC‐induced biomarkers and symptoms are reproducible and responsive to INCS. NAC is suitable for assessing pharmacodynamic activity and proof of mechanism for drugs targeting allergic inflammation.