Miracle-dz/UniFAR-FTUs huggingface dataset:
A Systematic Review of Glaucoma Diagnosis in Prevalence Studies and Quality of Reporting

Précis: This systematic review has revealed that variable definitions of glaucoma continue to be used in prevalence studies, despite the introduction of the International Society of Geographic and Epidemiologic Ophthalmology (ISGEO) criteria. Purpose: To systematically review diagnostic criteria and examinations performed in glaucoma prevalence studies over time and determine the quality of reporting. Accurate estimates of glaucoma prevalence are crucial to inform resource allocation. However, diagnosis of glaucoma comprises inherently subjective examinations and the cross-sectional nature of prevalence studies precludes monitoring for progression. Methods: A systematic review of PubMed, Embase, Web of Science, and Scopus was performed to examine diagnostic protocols used by glaucoma prevalence studies and evaluate uptake of the ISGEO criteria, introduced in 2002 to standardize glaucoma diagnosis in prevalence studies. Detection bias and compliance with the Strengthening Reporting of Observational Studies in Epidemiology (STROBE) guidelines were evaluated. Results: Ten thousand five hundred forty-four articles were identified. After deduplication, 5589 articles were screened, yielding 136 articles pertaining to 123 studies. An absence of data in many countries was identified. Ninety-two percent of studies stated diagnostic criteria, and 62% used the ISGEO criteria since their publication. Weaknesses of the ISGEO criteria were identified. Temporal variations in the performance of various examinations were observed, including heterogeneity in angle assessment. Mean STROBE compliance was 82% (range 59–100%); 72 articles had a low risk of detection bias, 4 had a high risk, and 60 had some concerns. Conclusion: Heterogeneous diagnostic definitions persist in glaucoma prevalence studies, despite introduction of the ISGEO criteria. Standardization of criteria remains imperative and the development of new criteria represent a valuable opportunity to achieve this goal. In addition, methods of determining diagnoses are poorly reported, suggesting a need for improvement in study conduct and reporting. Accordingly, we propose the Reporting of quality Of GlaUcoma Epidemiological Studies (ROGUES) Checklist. We have also identified a need for further prevalence studies in regions with limited data and to update Australian angle closure glaucoma prevalence. Design and reporting of future studies can be informed by this review’s insights into diagnostic protocols previously used.
Exploiting Diversity of Automatic Transcripts from Distinct Speech Recognition Techniques for Children’s Speech

The recent advances in automatic speech recognition (ASR) technologies using end-to-end machine learning do not transfer well to children’s speech. One cause is the high pronunciation variability and frequent violations of grammatical or lexical rules, which impedes the successful usage of language models or powerful context-representations. Applying these methods affects the nature of the resulting transcript rather than improving the overall recognition performance. In this work we analyze the diversity of the transcripts from distinct ASR-systems for children’s speech and exploit it by applying a common combination scheme. We consider systems with various degree of context: Greedily decoded and lexicon-constrained connection-ist temporal classification-models, attention-based encoder de-coders, and Wav2Vec 2.0, a powerful context-representation. By exploiting their diversity we achieve a relative improvement of 17.8% on phone recognition compared to the best single sys-tem.
Automatic pronunciation assessment vs. automatic speech recognition: A study of conflicting conditions for L2-English

This study addresses the issue of automatic pronunciation assessment (APA) and its contribution to the teaching of second language (L2) pronunciation. Several attempts have been made at designing such systems, and some have proven operationally successful. However, the automatic assessment of the pronunciation of short words in segmental approaches has still remained a significant challenge. Free and off-the-shelf automatic speech recognition (ASR) systems have been used in integration with other tools with the hopes of facilitating improvement in the domain of computer-assisted pronunciation training (CAPT). The use of ASR in APA stands on the premise that a word that is recognized is intelligible and well-pronounced. Our goal was to explore and test the functionality of Google ASR as the core component within a possible automatic British English pronunciation assessment system. After testing the system against standard and non-standard (foreign) pronunciations provided by participating pronunciation experts as well as non-expert native and non-native speakers of English, we found that Google ASR does not and cannot simultaneously meet two necessary conditions (here defined as intrinsic and derived) for performing as an APA system. Our study concludes with a synthetic view on the requirements of a reliable APA system.
Extracellular Vesicle–Encapsulated Adeno-Associated Viruses for Therapeutic Gene Delivery to the Heart

BACKGROUND: Adeno-associated virus (AAV) has emerged as one of the best tools for cardiac gene delivery due to its cardiotropism, long-term expression, and safety. However, a significant challenge to its successful clinical use is preexisting neutralizing antibodies (NAbs), which bind to free AAVs, prevent efficient gene transduction, and reduce or negate therapeutic effects. Here we describe extracellular vesicle–encapsulated AAVs (EV-AAVs), secreted naturally by AAV-producing cells, as a superior cardiac gene delivery vector that delivers more genes and offers higher NAb resistance. METHODS: We developed a 2-step density-gradient ultracentrifugation method to isolate highly purified EV-AAVs. We compared the gene delivery and therapeutic efficacy of EV-AAVs with an equal titer of free AAVs in the presence of NAbs, both in vitro and in vivo. In addition, we investigated the mechanism of EV-AAV uptake in human left ventricular and human induced pluripotent stem cell-derived cardiomyocytes in vitro and mouse models in vivo using a combination of biochemical techniques, flow cytometry, and immunofluorescence imaging. RESULTS: Using cardiotropic AAV serotypes 6 and 9 and several reporter constructs, we demonstrated that EV-AAVs deliver significantly higher quantities of genes than AAVs in the presence of NAbs, both to human left ventricular and human induced pluripotent stem cell-derived cardiomyocytes in vitro and to mouse hearts in vivo. Intramyocardial delivery of EV-AAV9–sarcoplasmic reticulum calcium ATPase 2a to infarcted hearts in preimmunized mice significantly improved ejection fraction and fractional shortening compared with AAV9–sarcoplasmic reticulum calcium ATPase 2a delivery. These data validated NAb evasion by and therapeutic efficacy of EV-AAV9 vectors. Trafficking studies using human induced pluripotent stem cell–derived cells in vitro and mouse hearts in vivo showed significantly higher expression of EV-AAV6/9–delivered genes in cardiomyocytes compared with noncardiomyocytes, even with comparable cellular uptake. Using cellular subfraction analyses and pH-sensitive dyes, we discovered that EV-AAVs were internalized into acidic endosomal compartments of cardiomyocytes for releasing and acidifying AAVs for their nuclear uptake. CONCLUSIONS: Together, using 5 different in vitro and in vivo model systems, we demonstrate significantly higher potency and therapeutic efficacy of EV-AAV vectors compared with free AAVs in the presence of NAbs. These results establish the potential of EV-AAV vectors as a gene delivery tool to treat heart failure.
Heterogeneous (Cu-Ti) colliding plasma dynamics

Laser ablated copper-titanium colliding plasma plume expansion at 10−4, 10−2, and 100 mbar of oxygen ambient pressures has been investigated with a view to understanding heterogeneous colliding plasma plume dynamics and the formation of multi-element stagnation layers using optical emission spectroscopy and fast imaging of plume. The observation of Cu2(A−X) and TiO−γ bands and their ambient pressure dependent emission intensity opens up the possibility of the stoichiometrically controlled formation of nanoclusters/nanocomposites.
Practical strategies for robust and inexpensive imaging of aqueous‐cleared tissues

Lightsheet microscopy offers an ideal method for imaging of large (mm–cm scale) biological tissues rendered transparent via optical clearing protocols. However the diversity of clearing technologies and tissue types, and how these are adapted to the microscope can make tissue mounting complicated and somewhat irreproducible. Tissue preparation for imaging can involve glues and or equilibration in a variety of expensive and/or proprietary formulations. Here we present practical advice for mounting and capping cleared tissues in optical cuvettes for macroscopic imaging, providing a standardised 3D cell that can be imaged routinely and relatively inexpensively. We show that acrylic cuvettes cause minimal spherical aberration with objective numerical apertures less than 0.65. Furthermore, we describe methods for aligning and assessing the light sheets, discriminating fluorescence from autofluorescence, identifying chromatic artefacts due to differential scattering and removing streak artefacts such that they do not confound downstream 3D object segmentation analyses, with mouse embryo, liver and heart imaging as demonstrated examples.
Emergence and retention of a collective memory in cockroaches

The stability of collective decisions-making in social systems is crucial as it can lead to counterintuitive phenomena such as collective memories, where an initial choice is challenged by environmental changes. Many social species face the challenge to perform collective decisions under variable conditions. In this study, we focused on situations where isolated individuals and groups of the American cockroach (Periplaneta americana) had to choose between two shelters with different luminosities that were inverted during the experiment. The darker shelter was initially preferred, but only groups that reached a consensus within that shelter maintain their choice after the light inversion, while isolated individuals and small groups lacked site fidelity. Our mathematical model, incorporating deterministic and probabilistic elements, sheds light on the significance interactions and their stochasticity in the emergence and retention of a collective memory.
Assessing the impact of recombination on the estimation of isolation-with-migration models using genomic data: a simulation study

Recombination events complicate the evolutionary history of populations and species and have a significant impact on the inference of isolation-with-migration (IM) models. However, several existing methods have been developed, assuming no recombination within a locus and free recombination between loci. In this study, we investigated the effect of recombination on the estimation of IM models using genomic data. We conducted a simulation study to evaluate the consistency of the parameter estimators with up to 1,000 loci and analyze true gene trees to examine the sources of errors in estimating the IM model parameters. The results showed that the presence of recombination led to biased estimates of the IM model parameters, with population sizes being more overestimated and migration rates being more underestimated as the number of loci increased. The magnitude of the biases tended to increase with the recombination rates when using 100 or more loci. On the other hand, the estimation of splitting times remained consistent as the number of loci increased. In the absence of recombination, the estimators of the IM model parameters remained consistent.
Evolutionarily conserved amino acids in MHC-II mediate bat influenza A virus entry into human cells

The viral hemagglutinins of conventional influenza A viruses (IAVs) bind to sialylated glycans on host cell surfaces for attachment and subsequent infection. In contrast, hemagglutinins of bat-derived IAVs target major histocompatibility complex class II (MHC-II) for cell entry. MHC-II proteins from various vertebrate species can facilitate infection with the bat IAV H18N11. Yet, it has been difficult to biochemically determine the H18:MHC-II binding. Here, we followed a different approach and generated MHC-II chimeras from the human leukocyte antigen DR (HLA-DR), which supports H18-mediated entry, and the nonclassical MHC-II molecule HLA-DM, which does not. In this context, viral entry was supported only by a chimera containing the HLA-DR α1, α2, and β1 domains. Subsequent modeling of the H18:HLA-DR interaction identified the α2 domain as central for this interaction. Further mutational analyses revealed highly conserved amino acids within loop 4 (N149) and β-sheet 6 (V190) of the α2 domain as critical for virus entry. This suggests that conserved residues in the α1, α2, and β1 domains of MHC-II mediate H18-binding and virus propagation. The conservation of MHC-II amino acids, which are critical for H18N11 binding, may explain the broad species specificity of this virus.
Tests for One-Sample Sensitivity and Specificity

The power analysis of a diagnostic test is often based on the sensitivity and specificity of the test. In such a test, the outcome of the diagnostic screening test is compared to the gold standard. In the common casecontrol study, the gold standard must be known before. In a prospective study, the gold standard is determined subsequent to the study, so the case-control framework is not appropriate. In this procedure, the power analysis and sample size requirements of such a design are considered.
Impact of Lens Opacity on Optical Coherence Tomography Angiography Metrics

Abstract Purpose To evaluate the impact of lens opacity on the reliability of optical coherence tomography angiography metrics and to find a vessel caliber threshold that is reproducible in cataract patients. Methods A prospective cohort study of 31 patients, examining one eye per patient, by applying 3 × 3 mm macular optical coherence tomography angiography before (18.94 ± 12.22 days) and 3 months (111 ± 23.45 days) after uncomplicated cataract surgery. We extracted superficial (SVC) and deep vascular plexuses (DVC) for further analysis and evaluated changes in image contrast, vessel metrics (perfusion density, flow deficit and vessel-diameter index) and foveal avascular area (FAZ). Results After surgery, the blood flow signal in smaller capillaries was enhanced as image contrast improved. Signal strength correlated to average lens density defined by objective measurement in Scheimpflug images (Pearson’s r: –.40, p: .027) and to flow deficit (r= –.70, p < .001). Perfusion density correlated to the signal strength index (r = .70, p < .001). Vessel metrics and FAZ area, except for FAZ area in DVC, were significantly different after cataract surgery, but the mean change was approximately 3–6%. A stepwise approach in extracting vessels according to their pixel caliber showed a threshold of > 6 pixels caliber (∼20–30 µm) was comparable before and after lens removal. Conclusion In patients with cataract, OCTA vessel metrics should be interpreted with caution. In addition to signal strength, contrast and pixel properties can serve as supplementary quality metrics to improve the interpretation of OCTA metrics. Vessels with ∼20–30 µm in caliber seem to be reproducible.
Stochastic equations and cities

Stochastic equations constitute a major ingredient in many branches of science, from physics to biology and engineering. Not surprisingly, they appear in many quantitative studies of complex systems. In particular, this type of equation is useful for understanding the dynamics of urban population. Empirically, the population of cities follows a seemingly universal law—called Zipf’s law—which was discovered about a century ago and states that when sorted in decreasing order, the population of a city varies as the inverse of its rank. Recent data however showed that this law is only approximate and in some cases not even verified. In addition, the ranks of cities follow a turbulent dynamics: some cities rise while other fall and disappear. Both these aspects—Zipf’s law (and deviations around it), and the turbulent dynamics of ranks—need to be explained by the same theoretical framework and it is natural to look for the equation that governs the evolution of urban populations. We will review here the main theoretical attempts based on stochastic equations to describe these empirical facts. We start with the simple Gibrat model that introduces random growth rates, and we will then discuss the Gabaix model that adds friction for allowing the existence of a stationary distribution. Concerning the dynamics of ranks, we will discuss a phenomenological stochastic equation that describes rank variations in many systems—including cities—and displays a noise-induced transition. We then illustrate the importance of exchanges between the constituents of the system with the diffusion with noise equation. We will explicit this in the case of cities where a stochastic equation for populations can be derived from first principles and confirms the crucial importance of inter-urban migrations shocks for explaining the statistics and the dynamics of the population of cities.
Occurrence and subsequent development of vertical deviations in patients treated surgically for infantile esotropia

Purpose: The purpose of this study was to evaluate the onset of dissociated vertical deviation (DVD) and inferior oblique overaction (IOOA), their subsequent development, and their correlation with pre and postoperative parameters. Methods: Medical records of patients with infantile esotropia who underwent surgery between 2005 and 2017 were retrospectively reviewed. DVD and IOOA were measured before and after surgery. Patients were divided into two groups based on horizontal and vertical deviation at the time of presentation: those with infantile esotropia only (group A) and patients with infantile esotropia who developed vertical deviation (group B). Results: Out of a total of 102 patients, DVD occurrence was seen in 53 patients (51.9%) and IOOA was seen in 50 patients (48.04%). DVD was seen in 22 patients at the time of initial examination and in 31 patients postoperatively. IOOA at presentation was seen in 45 patients (44.1%) and 5 patients (8.8%) postoperatively. No statistical difference was found in the age of surgery, angle of deviation, mean follow-up, and mean refractive error within both groups. The postoperative motor outcome was statistically comparable between the two groups (P = 0.29). Sensory outcomes of fusion (P = 0.048) and stereopsis (P-value = 0.00063) were better in group A. Conclusion: No correlation was found between the age of occurrence and development of vertical deviation with refractive error, angle of deviation, age, or type of surgery. We found that motor outcomes are not affected but sensory outcomes are affected in patients with vertical deviations. This indicates that DVD and IOOA are developed due to inherent disruption of fusion and stereopsis.
A computationally-inexpensive strategy in CT image data augmentation for robust deep learning classification in the early stages of an outbreak

Coronavirus disease 2019 (COVID-19) has spread globally for over three years, and chest computed tomography (CT) has been used to diagnose COVID-19 and identify lung damage in COVID-19 patients. Given its widespread, CT will remain a common diagnostic tool in future pandemics, but its effectiveness at the beginning of any pandemic will depend strongly on the ability to classify CT scans quickly and correctly when only limited resources are available, as it will happen inevitably again in future pandemics. Here, we resort into the transfer learning procedure and limited hyperparameters to use as few computing resources as possible for COVID-19 CT images classification. Advanced Normalisation Tools (ANTs) are used to synthesise images as augmented/independent data and trained on EfficientNet to investigate the effect of synthetic images. On the COVID-CT dataset, classification accuracy increases from 91.15% to 95.50% and Area Under the Receiver Operating Characteristic (AUC) from 96.40% to 98.54%. We also customise a small dataset to simulate data collected in the early stages of the outbreak and report an improvement in accuracy from 85.95% to 94.32% and AUC from 93.21% to 98.61%. This study provides a feasible Low-Threshold, Easy-To-Deploy and Ready-To-Use solution with a relatively low computational cost for medical image classification at an early stage of an outbreak in which scarce data are available and traditional data augmentation may fail. Hence, it would be most suitable for low-resource settings.
Rapid Determination of Three Organic Acids in Polygonum Vivipari Rhizoma via One Marker by HPLC-UV at Equal Absorption Wavelength and Effervescence-Assisted Matrix Solid-Phase Dispersion

A rapid HPLC-UV method for the determination of three organic acids (neochlorogenic acid, chlorogenic acid, and cryptochlorogenic acid) in Polygoni Vivipari Rhizoma (PVR) by one marker was developed. The sample was prepared by effervescence-assisted matrix solid-phase dispersion (EA-MSPD). The separation of compounds was performed on a Poroshell column. The equal absorption wavelength was set as follows: 292 nm (0∼7 min) and 324 nm (7∼10 min). The analytical time including sample extraction and HPLC separation time was 12 min. The analytical method validation such as accuracy (recoveries 99.85%–106.29% and RSD < 2.9%), precision (RSD < 1.3%), reproducibility (RSD < 1.7%), and stability tests (RSD < 0.7% in 24 h) proved that the established HPLC method was suitable for determination of three organic acids in PVR. The contents of three analytes obtained by the external standard method with three markers and the equal absorption wavelength method with one marker were similar (RSD ≤ 2.0%). The developed method, which is rapid and reference compound saving, is an improved quality evaluation method of PVR.
Improved Configurations for 3D Acoustoelectric Tomography With a Minimal Number of Electrodes

Objective: Acoustoelectric tomography (AET) is a hybrid imaging technique combining ultrasound and electrical impedance tomography (EIT). It exploits the acoustoelectric effect (AAE): an US wave propagating through the medium induces a local change in conductivity, depending on the acoustoelectric properties of the medium. Typically, AET image reconstruction is limited to 2D and most cases employ a large number of surface electrodes. Methods: This article investigates the detectability of contrasts in AET. We characterize the AEE signal as a function of the medium conductivity and electrode placement, using a novel 3D analytical model of the AET forward problem. The proposed model is compared to a finite element method simulation. Results: In a cylindrical geometry with an inclusion contrast of 5 times the background and two pairs of electrodes, the maximum, minimum, and mean suppression of the AEE signal are 68.5%, 3.12%, and 49.0%, respectively, over a random scan of electrode positions. The proposed model is compared to a finite element method simulation and the minimum mesh sizes required successfully model the signal is estimated. Conclusion: We show that the coupling of AAE and EIT leads to a suppressed signal and the magnitude of the reduction is a function of geometry of the medium, contrast and electrode locations. Significance: This model can aid in the reconstruction of AET images involving a minimum number of electrodes to determine the optimal electrode placement.