Miracle-dz/UniFAR-FTUs huggingface dataset:
Blind validation of MSIntuit, an AI-based pre-screening tool for MSI detection from histology slides of colorectal cancer

Objective: Mismatch Repair Deficiency (dMMR) / Microsatellite Instability (MSI) is a key biomarker in colorectal cancer (CRC). Universal screening of CRC patients for dMMR/MSI status is now recommended, but contributes to increased workload for pathologists and delayed therapeutic decisions. Deep learning has the potential to ease dMMR/MSI testing in clinical practice, yet no comprehensive validation of a clinically approved tool has been conducted. Design: We developed an MSI pre-screening tool, MSIntuit, that uses deep learning to identify MSI status from H&E slides. For training, we used 859 slides from the TCGA database. A blind validation was subsequently performed on an independent dataset of 600 consecutive CRC patients. Each slide was digitised using Phillips-UFS and Ventana-DP200 scanners. Thirty dMMR/MSI slides were used for calibration on each scanner. Prediction was then performed on the remaining 570 patients following an automated quality check step. The inter and intra-scanner reliability was studied to assess MSIntuit's robustness. Results: MSIntuit reached a sensitivity and specificity of 97% (95% CI: 93-100%) / 46% (42-50%) on DP200 and of 95% (90-98%) / 47% (43-51%) on UFS scanner. MSIntuit reached excellent agreement on the two scanners (Cohen's {kappa}: 0.82) and was repeatable across multiple rescanning of the same slide (Fleiss' {kappa}: 0.82). Conclusion: We performed a successful blind validation of the first clinically approved AI-based tool for MSI detection from H&E slides. MSIntuit reaches sensitivity comparable to gold standard methods (92-95%) while ruling out almost half of the non-MSI population, paving the way for its use in clinical practice.
Red Supergiants in the JWST Era. I. Near-IR Photometric Diagnostics

The Near Infrared Camera (NIRCam) on the James Webb Space Telescope (JWST) will be an incredibly powerful instrument for studying red supergiants (RSGs). The high luminosities and red peak wavelengths of these stars make them ideal targets for JWST/NIRCam. With effective photometric diagnostics in place, imaging RSG populations in multiple filters will make it possible to determine these stars’ physical properties and, in cases where JWST pre-explosion imaging is available, to identify RSG supernova progenitors. This paper uses observed and model spectra of Galactic RSGs to simulate JWST/NIRCam near-IR photometry and colors, quantify and test potential diagnostics of effective temperature and bolometric magnitude, and present photometric techniques for separating background RSG and foreground dwarf populations. While results are presented for the full suite of near-IR filters, this work shows that (F070W–F200W) is the JWST/NIRCam color index most sensitive to effective temperature, F090W is the best band for determining bolometric magnitude, and the (F070W–F090W) versus (F090W–F200W) color–color diagram can be used to separate foreground dwarf and background RSG samples. The combination of these three filters is recommended as the best suite of photometric observations to use when studying RSGs with JWST.
Creation of Theta-Auroras: The Isolation of Plasma Sheet Fragments in the Polar Cap

The auroral oval is a ring of luminosity enclosing geomagnetic field lines connected to the solar wind. Occasionally the ring has a bar across it, which seems to imply a bifurcation of the open region. Here results confirm that this “θ-aurora” actually does represent this odd bifurcated configuration, and they demonstrate how it happens. It has hitherto been assumed that θ-auroras occur when the interplanetary magnetic field is directed northward, because that is true of most very-high-latitude arcs. In fact, θ-auroras occur exclusively during the dynamic reconfiguration that follows when the interplanetary magnetic field turns southward after a prolonged northward interval.
High Spatial Resolution Time-of-Flight Secondary Ion Mass Spectrometry for the Masses: A Novel Orthogonal ToF FIB-SIMS Instrument with In Situ AFM

We describe the design and performance of an orthogonal time-of-flight (TOF) secondary ion mass spectrometer that can be retrofitted to existing focused ion beam (FIB) instruments. In particular, a simple interface has been developed for FIB/SEM instruments from the manufacturer Tescan. Orthogonal extraction to the mass analyser obviates the need to pulse the primary ion beam and does not require the use of monoisotopic gallium to preserve mass resolution. The high-duty cycle and reasonable collection efficiency of the new instrument combined with the high spatial resolution of a gallium liquid metal ion source allow chemical observation of features smaller than 50 nm. We have also demonstrated the integration of a scanning probe microscope (SPM) operated as an atomic force microscope (AFM) within the FIB/SEM-SIMS chamber. This provides roughness information, and will also allow true three dimensional chemical images to be reconstructed from SIMS measurements.
New integrable structures in large-N QCD

We study the anomalous dimensions of single trace operators composed of field strengths $F_{\mu\nu}$ in large-N QCD. The matrix of anomalous dimensions is the Hamiltonian of a compact spin chain with two spin one representations at each vertex corresponding to the selfdual and anti-selfdual components of $F_{\mu\nu}$. Due to the special form of the interaction it is possible to study separately renormalization of purely selfdual components. In this sector the Hamiltonian is integrable and can be exactly solved by Bethe ansatz. Its continuum limit is described by the level two SU(2) WZW model.
Evolution of dust extinction curves in galaxy simulation

To understand the evolution of extinction curve, we calculate the dust evolution in a galaxy using smoothed particle hydrodynamics simulations incorporating stellar dust production, dust destruction in supernova shocks, grain growth by accretion and coagulation, and grain disruption by shattering. The dust species are separated into carbonaceous dust and silicate. The evolution of grain size distribution is considered by dividing grain population into large and small gains, which allows us to estimate extinction curves. We examine the dependence of extinction curves on the position, gas density, and metallicity in the galaxy, and find that extinction curves are flat at $t \lesssim 0.3$ Gyr because stellar dust production dominates the total dust abundance. The 2175 \AA\ bump and far-ultraviolet (FUV) rise become prominent after dust growth by accretion. At $t \gtrsim 3$ Gyr, shattering works efficiently in the outer disc and low density regions, so extinction curves show a very strong 2175 \AA\ bump and steep FUV rise. The extinction curves at $t\gtrsim 3$ Gyr are consistent with the Milky Way extinction curve, which implies that we successfully included the necessary dust processes in the model. The outer disc component caused by stellar feedback has an extinction curves with a weaker 2175 \AA\ bump and flatter FUV slope. The strong contribution of carbonaceous dust tends to underproduce the FUV rise in the Small Magellanic Cloud extinction curve, which supports selective loss of small carbonaceous dust in the galaxy. The snapshot at young ages also explain the extinction curves in high-redshift quasars.
Latin American Internet Survey for Men who have Sex with Men (LAMIS-2018): Design, methods and implementation

Despite men-who-have-sex-with-men (MSM) from Latin America (LA) are still a vulnerable population for known health-related conditions and social problems, availability of comparable data across LA countries for assessment and monitoring purposes is limited. The objective of this article is to present the study design and the questionnaire of LAMIS-2018 (Latin America MSM Internet Survey), its recruitment strategy, rates and sources by country, and the lessons learned from its implementation. LAMIS-2018 was a cross-sectional, internet-based survey targeting MSM living in 18 LA countries (Argentina, Bolivia, Brazil, Chile, Colombia, Costa Rica, Ecuador, El Salvador, Guatemala, Honduras, Mexico, Nicaragua, Panama, Paraguay, Peru, Suriname, Uruguay, and Venezuela) that gathered data about sexual behaviors, HIV/STI and viral hepatitis knowledge, prophylactic use of antiretrovirals, psychosocial health, and access to sexual health services. The survey went online for four months and was available in three languages (Spanish, Portuguese, and Dutch). Promotion was carried out using dating apps, websites, social networks, and by community-based and academic organizations of each participating country directly in gay venues and in their own premises. Overall, 64,655 MSM participated in LAMIS-2018. Dating apps and websites were the most important recruitment source in most countries, except for Honduras, Nicaragua, and Suriname, where community-based organizations recruited most of the participants. Beyond the LAMIS-2018 implementation description, we highlight the feasibility of such a study in this context, based on the collaboration between community-based and academic organizations to obtain a large sample of MSM in the region. LAMIS-2018 data will contribute to identify determinants of risk behaviors and prevention needs of vulnerable MSM populations in each country of the region.
Covid-19 vaccines in Italian public opinion: Identifying key issues using Twitter and Natural Language Processing

The COVID-19 pandemic has changed society and people’s lives. The vaccination campaign started December 27th 2020 in Italy, together with most countries in the European Union. Social media platforms can offer relevant information about how citizens have experienced and perceived the availability of vaccines and the start of the vaccination campaign. This study aims to use machine learning methods to extract sentiments and topics relating to COVID-19 vaccination from Twitter. Between February and May 2021, we collected over 71,000 tweets containing vaccines-related keywords from Italian Twitter users. To get the dominant sentiment throughout the Italian population, spatial and temporal sentiment analysis was performed using VADER, highlighting sentiment fluctuations strongly influenced by news of vaccines’ side effects. Additionally, we investigated the opinions of Italians with respect to different vaccine brands. As a result, ‘Oxford-AstraZeneca’ vaccine was the least appreciated among people. The application of the Dynamic Latent Dirichlet Allocation (DLDA) model revealed three fundamental topics, which remained stable over time: vaccination plan info, usefulness of vaccinating and concerns about vaccines (risks, side effects and safety). To the best of our current knowledge, this one the first study on Twitter to identify opinions about COVID-19 vaccination in Italy and their progression over the first months of the vaccination campaign. Our results can help policymakers and research communities track public attitudes towards COVID-19 vaccines and help them make decisions to promote the vaccination campaign.
Predicting the hypervelocity star population in Gaia

Hypervelocity stars (HVSs) are amongst the fastest objects in our Milky Way. These stars are predicted to come from the Galactic center (GC) and travel along unbound orbits across the Galaxy. In the coming years, the ESA satellite Gaia will provide the most complete and accurate catalogue of the Milky Way, with full astrometric parameters for more than $1$ billion stars. In this paper, we present the expected sample size and properties (mass, magnitude, spatial, velocity distributions) of HVSs in the Gaia stellar catalogue. We build three Gaia mock catalogues of HVSs anchored to current observations, exploring different ejection mechanisms and GC stellar population properties. In all cases, we predict hundreds to thousands of HVSs with precise proper motion measurements within a few tens of kpc from us. For stars with a relative error in total proper motion below $10 \%$, the mass range extends to ~$10 M_{\odot}$ but peaks at ~$1$ $M_\odot$. The majority of Gaia HVSs will therefore probe a different mass and distance range compared to the current non-Gaia sample. In addition, a subset of a few hundreds to a few thousands of HVSs with $M$ ~ $3$ $M_\odot$ will be bright enough to have a precise measurement of the three-dimensional velocity from Gaia alone. Finally, we show that Gaia will provide more precise proper motion measurements for the current sample of HVS candidates. This will help identifying their birthplace narrowing down their ejection location, and confirming or rejecting their nature as HVSs. Overall, our forecasts are extremely encouraging in terms of quantity and quality of HVS data that can be exploited to constrain both the Milky Way potential and the GC properties.
Diagnostic yield, complications, pathology and anatomical features in CT-guided percutaneous needle biopsy of mediastinal tumours

Objectives This study presents the experiences of percutaneous CT-guided needle biopsy at a university hospital in Norway. Methods A retrospective examination of all mediastinal biopsy procedures between April 2015 and August 2019 was performed at Akershus University Hospital in Norway. We registered patient and procedure characteristics, along with lesion pathology and characteristics including localization according to anatomical and Felson mediastinal compartments. Results The study included 48 procedures, conducted in 45 patients (29 men and 16 women) with a mean age of 60,5 years. Pneumothorax occurred in 12 procedures (60% of the transpulmonary procedures) and pneumomediastinum in 18 procedures (38%). Pneumothorax was only seen in procedures with transpulmonal access. Four of the pneumothorax cases required pleural drainage. Diagnostic yield was 96%. We found significant (p = 0,006), moderate to high association between anatomical compartment localization and histopathological diagnosis (Cramér’s V = 0,49) for tumours selected for CT-guided percutaneous biopsy. Felson’s compartment division on the other hand, did not show any significant associations. Conclusion We found CT-guided percutaneous needle biopsy of mediastinal tumours to be an effective and safe procedure with a diagnostic yield of 96%. The main complications were pneumothorax and pnumomediastinum, with a relatively low chest drainage rate. Anatomical mediastinum compartment showed a significant, moderate to high association with the histopathological diagnosis for tumours selected for percutaneous CT-guided biopsies, where most malignancies were seen in the anterior compartment.
Census of Twitter users: Scraping and describing the national network of South Korea

Population-level national networks on social media are precious and essential for network science and behavioural science. This study collected a population-level Twitter network, based on both language and geolocation tags. We proposed a set of validation approaches to evaluate the validity of our datasets. Finally, we re-examined classical network and communication propositions (e.g., 80/20 rule, six degrees of separation) on the national network. Our dataset and strategy would flourish the data collection pool of population-level social networks and further develop the research of network analysis in digital media environment.
New insights into the impact of financial inclusion on economic growth: A global perspective

Financial inclusion is critical to inclusive growth, proffering policy solutions to eradicate the barriers that exclude individuals from financial markets. This study explores the effects of financial inclusion on economic growth in a global perspective with a large number of panels classified by income and regional levels from 2002–2020. The analysis begins with the development of a comprehensive composite financial inclusion index comprised of penetration, availability, and usage of financial services and the estimation of heterogeneous panel data models augmented with well-known variables. The results obtained from the panel cointegration test support a long-run relationship between economic growth, financial inclusion, and the control variables in the full panel, income-level, and regional-level economies. Furthermore, the study employs a GMM (generalized method of moment) approach using System-GMM estimators to examine the effects of financial inclusion and the control predictors on economic growth. The results of the GMM model clearly indicate that financial inclusion has a significantly positive impact on economic growth across all panels, implying that financial inclusion is an effective tool in fostering rapid economic growth in the world. Finally, the study delves into the causality relationship between the predictors and provides statistical evidence of bidirectional causality between economic growth and financial inclusion, whereas it only supports unidirectional causality relationships from credit to the private sector, foreign direct investment, inflation rate, the rule of law, school enrollment ratio, and trade openness with no feedback causality. Moreover, the study fails to provide causality evidence from the age dependency ratio and population to economic growth.
Is it really a piece of cake to label Geographical Indications with the Nutri-Score? Consumers’ behaviour and policy implications

To improve the dietary habits of the population, the EU, within the Farm to Fork strategy (F2F), is strongly supporting the Nutri-Score (NS) Front Of Pack (FOP) label. Under the NS system, Geographical Indications (GIs) are generally scored as “unhealthy” food, given the predominance of products of animal origin among GIs which are, notoriously, high-fat products. This study aims to determine the impact of the NS label on consumers’ preferences for two Protected Designation of Origin (PDO) cheeses, in comparison with generic ones. A Discrete Choice Experiment (DCE) was conducted on 600 Italian consumers through the estimation of a Random Parameter Logit model. Results highlighted that Italian consumers are generally not familiar with the NS and perceive it as a positive characteristic of the product, even if it is signalling an unhealthy choice (D score). However, consumers aware of the Nutri-Score meaning are willing to pay less to buy a product considered “unhealthy” according to this system. Furthermore, we found that consumers who already knew the NS system have homogeneous behaviours in rejecting the product, independently of the association with a PDO certification. This result has important implications on the agri-food sector. If the Nutri-Score becomes mandatory in the EU, consumers might refuse many GIs due to their negative Nutri-Score values. However, the quality of these products is recognized and protected worldwide. In this vein, the GI policy could be questioned by the F2F strategy: both of them aims to reduce information asymmetry producing, at the same time, contrasting results. Within the Geographical Indication policy, the PDO and PGI goods are protected for their quality attributes, which are strictly linked to their geographical origin of the products and traditional know-how. However, the EU adoption of the Nutri-Score could damage these products, reducing their perceived quality/value.
Incidence of HIV infection and associated factors among female sex workers in Côte d’Ivoire, results of the ANRS 12361 PrEP-CI study using recent infection assays

Background This study aimed to estimate, using an HIV Recent Infection Testing Algorithm (RITA), the HIV incidence and its associated factors among female sex workers (FSW) in Côte d’Ivoire. Methods A cross-sectional study was conducted in 2016–2017 in Abidjan and San Pedro’s region among FSW aged ≥ 18 years. In addition, a sociodemographic questionnaire, HIV screening was carried out by two rapid tests. In the event of a positive result, a dried blood spot sample was taken to determine, using a RITA adapted to the Ivorian context, if it was a recent HIV infection. Results A total of 1000 FSW were surveyed with a median age of 25 years (interquartile range: 21–29 years). 39 (3.9%) tested positive for HIV. The incidence of HIV was estimated to be 2.3 per 100 person-years, with higher incidence rates among those 24 years old or less (3.0% vs. 1.9%), non-Ivorian FSW (3.2% vs. 1.9%) and those with the lowest education level (4.6% in FSW who never went to school vs. 2.6%). The incidence seemed to be associated with the sex work practice conditions: higher incidence among FSW whose usual price was less than 3.50$ (4.3% vs.1.0%), FSW who had a larger number of clients on the last day of work (6.1% in those with 7 clients or more vs. 1.8%), FSW who reported not always using condoms with their clients (8.5% vs. 1.5%) and FSW who reported agreeing to sex without a condom in exchange for a large sum of money (10.1% vs. 1.2%). Conclusion This study confirms that FSW remain highly exposed to HIV infection. Exposure to HIV is also clearly associated with certain sex-work factors and the material conditions of sex work. Efforts in the fight against HIV infection must be intensified to reduce new infections among FSW.
The validity and reliability of wearable devices for the measurement of vertical oscillation for running

Wearable devices are a popular training tool to measure biomechanical performance indicators during running, including vertical oscillation (VO). VO is a contributing factor in running economy and injury risk, therefore VO feedback can have a positive impact on running performance. The validity and reliability of the VO measurements from wearable devices is crucial for them to be an effective training tool. The aims of this study were to test the validity and reliability of VO measurements from wearable devices against video analysis of a single trunk marker. Four wearable devices were compared: the INCUS NOVA, Garmin Heart Rate Monitor-Pro (HRM), Garmin Running Dynamics Pod (RDP), and Stryd Running Power Meter Footpod (Footpod). Fifteen participants completed treadmill running at five different self-selected speeds for one minute at each speed. Each speed interval was completed twice. VO was recorded simultaneously by video and the wearables devices. There was significant effect of measurement method on VO (p < 0.001), with the NOVA and Footpod underestimating VO compared to video analysis, while the HRM and RDP overestimated. Although there were significant differences in the average VO values, all devices were significantly correlated with the video analysis (R > = 0.51, p < 0.001). Significant agreement between repeated VO measurements for all devices, revealed the devices to be reliable (ICC > = 0.948, p < 0.001). There was also significant agreement for VO measurements between each device and the video analysis (ICC > = 0.731, p < = 0.001), therefore validating the devices for VO measurement during running. These results demonstrate that wearable devices are valid and reliable tools to detect changes in VO during running. However, VO measurements varied significantly between the different wearables tested and this should be considered when comparing VO values between devices.