Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Symbol Length of Fields with finite Square Class Number

Let $F$ be a field of characteristic not $2$ with finitely many square classes. Using combinatorial arguments applied to objects related to vector spaces over finite fields, we deduce an upper bound for the number of Pfister forms over $F$. Moreover, we compute upper bounds for the $n$-symbol length $F$ ($n\in\mathbb N$), i.e., the smallest integer $\mathrm{sl}_n(F)\geq 0$ such that to each quadratic form $\phi\in \mathsf I^n(F)$ there exists some $0\leq k\leq \mathrm{sl}_n(F)$ and Pfister forms $\pi_1,\ldots, \pi_k$ such that $\varphi\equiv \pi_1+\ldots+\pi_k\mod \mathsf I^{n+1}(F)$. In particular, we rediscover a bound that can also be deduced from a result by Bruno Kahn that he stated without proof.
Dopamine: Differentially Private Federated Learning on Medical Data

While rich medical datasets are hosted in hospitals distributed across the world, concerns on patients' privacy is a barrier against using such data to train deep neural networks (DNNs) for medical diagnostics. We propose Dopamine, a system to train DNNs on distributed datasets, which employs federated learning (FL) with differentially-private stochastic gradient descent (DPSGD), and, in combination with secure aggregation, can establish a better trade-off between differential privacy (DP) guarantee and DNN's accuracy than other approaches. Results on a diabetic retinopathy~(DR) task show that Dopamine provides a DP guarantee close to the centralized training counterpart, while achieving a better classification accuracy than FL with parallel DP where DPSGD is applied without coordination. Code is available at https://github.com/ipc-lab/private-ml-for-health.
Visible Light Communication Based Vehicle Localization for Collision Avoidance and Platooning

Collision avoidance and platooning applications require vehicle localization at cm-level accuracy and at least 50 Hz rate for full autonomy. The RADAR/LIDAR and camera based methods currently used for vehicle localization do not satisfy these requirements, necessitating complementary technologies. Visible light positioning (VLP) is a highly suitable complementary technology due to its high accuracy and high rate, exploiting the line-of-sight propagation feature of the visible light communication (VLC) signals from LED head/tail lights. However, existing vehicular VLP algorithms impose restrictive requirements, e.g., use of high-bandwidth circuits, road-side lights and certain VLC modulation strategies, and work for limited relative vehicle orientations, thus, are not feasible for general use. This paper proposes a VLC-based vehicle localization method that eliminates these restrictive requirements by a novel VLC receiver design and associated vehicular VLP algorithm. The VLC receiver, named QRX, is low-cost/size, and enables high-rate VLC and high-accuracy angle-of-arrival (AoA) measurement, simultaneously, via the usage of a quadrant photodiode. The VLP algorithm estimates the positions of two head/tail light VLC transmitters (TX) on a neighbouring vehicle by using AoA measurements from two QRXs for localization. The algorithm is theoretically analyzed by deriving its Cramer-Rao lower bound on positioning accuracy, and simulated localization performance is evaluated under realistic platooning and collision avoidance scenarios. Results demonstrate that the proposed method performs at cm-level accuracy and up to 250 Hz rate within a 10 m range under realistic harsh road and channel conditions, demonstrating its eligibility for collision avoidance and safe platooning.
Longitudinal Growth Differentiation Factor 15 (GDF15) and Long-term Intraocular Pressure Fluctuation in Glaucoma: A Pilot Study

Abstract Purpose Growth Differentiation Factor 15 (GDF15) was previously identified as a molecular marker of retinal ganglion cell stress in rodent models of glaucoma and was elevated in the aqueous humor (AH) of patients with primary open-angle glaucoma as a possible risk factor for glaucoma progression. The purpose of this study was to determine whether changes in the AH GDF15 levels were associated with intraocular pressure (IOP) changes in eyes undergoing glaucoma surgery. Methods Here, we performed a prospective, longitudinal pilot study in nine patients to determine whether changes in AH GDF15 levels from surgery to post-surgery follow-up were associated with IOP fluctuation. An initial AH sample was taken from the peripheral corneal paracentesis during planned glaucoma surgery, and a second sample was taken during an outpatient follow-up visit, approximately six months later. Results There was a statistically significant correlation between GDF15 fold change and IOP standard deviation (r = 0.87, P = 0.003), IOP range (r = 0.87, P = 0.003), and maximum IOP (r = 0.86, P = 0.003). There was no correlation between the GDF15 fold change and baseline IOP (r = 0.50, P = 0.17), final IOP (r = 0.038, P = 0.92), or mean IOP (r = 0.40, P = 0.28). Conclusion Our findings in this pilot study suggest that longitudinal changes in AH GDF15 may be associated with IOP fluctuation during the postoperative period. Further studies are necessary to corroborate these findings in a larger patient population and to explore the possibility that AH GDF15 may be used not only to improve treatment algorithms but also as a surrogate endpoint in clinical trials.
Multiplex PCR for Detection of Herpes Simplex Viruses Type-1 and Type-2, Cytomegalovirus, Varicella-zoster Virus, and Adenovirus in Ocular Viral Infections

Abstract Purpose Most common viruses causing ocular infections are Herpes Simplex Viruses (HSV) type 1 and type 2, Cytomegalovirus (CMV), Varicella-zoster Virus (VZV), and few strains of Adenovirus. Diagnosis of these infections through clinical manifestations and using conventional methods has a number of limitations. The purpose of this study was to develop a multiplex Polymerase Chain Reaction (PCR) for simultaneous detection of all pathogenic viruses from ocular infections. Methods Ten uniplex PCRs were standardized, two each for HSV type 1 (HSV-1) and type 2 (HSV-2), CMV, VZV, and Adenovirus. Various multiplexing combinations of above PCRs were put to finalize targets and reaction conditions enabling diagnosis of all in a single reaction. The uniplex and multiplex PCRs were run for known positive and negative controls, and samples from clinically suspected patients and healthy controls. Results Out of the 170 samples from suspected ocular infections, 24.7% were positive by uniplex PCR and 22.9% were correctly identified by multiplex PCR. None of the samples negative by uniplex PCRs was positive by the multiplex PCR. The sensitivity and specificity of multiplex PCR compared to the commonly used uniplex PCRs as gold standard was 92.86% and 100%, respectively. The prevalence of different viral pathogens was 13.5% for HSV-1, followed by 5.9% for Adenovirus, 2.4% for VZV, 1.8% for HSV-2, and 1.2% for CMV. Conclusion The establishment of multiplex PCR has found immediate application in diagnosing ocular viral pathogens in a single reaction, thus saving time, manpower, and resources by fivefold.
Dual short wavelength infrared transillumination/reflectance mode imaging for caries detection

Abstract. Significance: We have developed a clinical probe capable of acquiring near-simultaneous short-wavelength infrared (SWIR) reflectance and occlusal transillumination images of lesions on tooth proximal and occlusal surfaces. We hypothesize that dual images will aid in differentiating between shallow and deep occlusal lesions and reduce the potential of false positives (FPs). Aim: The aim of this study was to test the performance of the dual reflectance and occlusal transillumination probe on extracted teeth prior to commencing clinical studies. Approach: The dual probe was 3D printed and the imaging system uses an InGaAs camera and broadband superluminescent diode light sources that emit broadband light at 1300 nm for occlusal transillumination and 1600-nm light for cross-polarization reflectance. The diagnostic performance of the dual probe was assessed using 120 extracted teeth with approximal and occlusal lesions. Reflectance and transillumination images were fused into single images to enhance the contrast between sound and lesion areas. The lesion contrast in both modes did not increase significantly with either the lesion depth or the distance from the occlusal surface for approximal lesions. In addition, the diagnostic performance of radiography, the individual reflectance and transillumination images, dual images, and fused images were compared using micro-computed tomography as the gold standard. Results: Reflectance imaging at 1600 nm yielded the highest diagnostic accuracy for lesions on both occlusal and proximal surfaces while radiography yielded the lowest number of FPs. Conclusion: This study demonstrates that simultaneous acquisition of both reflectance and transillumination SWIR images is possible with a single clinical device.
Environmental Pollution and Chronic Kidney Disease

Chronic kidney disease (CKD) is a global public health problem associated with high rates of morbidity and mortality due to end-stage renal disease and cardiovascular disease. Safe and effective medications to reverse or stabilize renal function in patients with CKD are lacking, and hence it is important to identify modifiable risk factors associated with worsening kidney function. Environmental pollutants, including metals, air pollutant, phthalate and melamine can potentially increase the risk of CKD or accelerate its progression. In this review, we discuss the epidemiological evidence for the association between environmental pollution and kidney disease, including heavy metals, air pollution and other environmental nephrotoxicants in the general population.
Modelling carbon and nitrogen dynamics in a bare soil with and without straw incorporation

Incorporating straw into the ploughed layer of soil affects the dynamics of carbon and nitrogen. A precise quantification of its short‐term effect in agricultural fields is difficult because biological and physical processes interact and take place simultaneously. As an alternative to experimentation, investigations have turned to simulations using mechanistic models, and we have taken this approach. The goal of our study was to test a mechanistic and one‐dimensional model of transport and biotransformation (PASTIS) against a data set obtained in a field experiment in northern France. We tested carbon and nitrogen dynamics by measuring C mineralization rates, the rates of gross immobilization and mineralization of N (using 15N tracing), and inorganic pools of N in the soil profile during 1 year in a bare soil with or without addition of wheat straw. Most of the model parameters were determined in independent experiments. We estimated the biological parameters from incubation experiments in the laboratory. The simulated results were in good agreement with experimental data, particularly for gross N rates. Hypotheses concerning the pathway of microbial assimilation and the dependence of decomposition on the size of the biomass were tested. The simulated net N immobilization due to addition of straw (8000 kg dry matter ha−1) reached a maximum of 64 kg N ha−1 after 2 months, whereas the observed value was 66 kg N ha−1. The model indicated that after 13 months the incorporation of straw had reduced the net amount of nitrogen mineralized by 13% and the amount of leached nitrate by 27%. The sensitivity analysis to the depth of straw incorporation indicated that the deeper was the incorporation the less was the leaching and the mineralization of nitrogen.
The Effects of Time-Restricted Eating versus Standard Dietary Advice on Weight, Metabolic Health and the Consumption of Processed Food: A Pragmatic Randomised Controlled Trial in Community-Based Adults

The prevalence of metabolic syndrome (MS) is increasing, affecting approximately 1 billion people. Weight loss is key to control MS components, i.e. central obesity, hypertension, prediabetes, and dyslipidemia. Here, we characterised the relationships between eating duration, unprocessed and processed food consumption, and metabolic health. In a 4-week observation phase, 213 Swiss adults recorded consumed meals and drinks with a smartphone application, and these were annotated for food processing levels according to the NOVA classification. Regression analysis showed that the number of unprocessed food items showed the highest number of significant relationships with MS components after age and sex. Next, in a randomised controlled trial, we tested whether 12-hour time-restricted eating (TRE) for 6 months leads to metabolic benefits compared to standard dietary advice (SDA), in adults who ate >14h per 24h cycle and had at least one MS component. Twenty-eight adults were randomised to TRE and lost 1.6% of initial body weight (SD 3.0%, p = 0.02), compared to the 26 in the SDA arm whose weight was stable (-1.1%, SD 3.4%, p = 0.17). No significant difference in body weight reduction was observed between TRE and SDA (p = 0.56). Overall, our results show the promise of smartphone records to predict metabolic health, and highlight that further research is needed to understand individual responses to TRE and SDA.
Comparative performance of multiplex salivary and commercially available serologic assays to detect SARS-CoV-2 IgG and neutralization titers

Oral fluid (hereafter saliva) offers a non-invasive sampling method for the detection of SARS-CoV-2 antibodies. However, data comparing performance of salivary tests against commercially-available serologic and neutralizing antibody (nAb) assays are lacking. This study compared the performance of a multiplex salivary SARS-CoV-2 IgG assay targeting antibodies to nucleocapsid (N), receptor binding domain (RBD) and spike (S) antigens to three commercially-available SARS-CoV-2 serology enzyme immunoassays (EIAs) (Ortho Vitros, Euroimmun, and BioRad) and nAb. Paired saliva and plasma samples were collected from 101 eligible COVID-19 convalescent plasma (CCP) donors >14 days since PCR+ confirmed diagnosis. Concordance was evaluated using positive (PPA) and negative (NPA) percent agreement, overall percent agreement (PA), and Cohen kappa coefficient. The range between salivary and plasma EIAs for SARS-CoV-2-specific N was PPA: 54.4-92.1% and NPA: 69.2-91.7%, for RBD was PPA: 89.9-100% and NPA: 50.0-84.6%, and for S was PPA: 50.6-96.6% and NPA: 50.0-100%. Compared to a plasma nAb assay, the multiplex salivary assay PPA ranged from 62.3% (N) and 98.6% (RBD) and NPA ranged from 18.8% (RBD) to 96.9% (S). Combinations of N, RBD, and S and a summary algorithmic index of all three (N/RBD/S) in saliva produced ranges of PPA: 87.6-98.9% and NPA: 50-91.7% with the three EIAs and ranges of PPA: 88.4-98.6% and NPA: 21.9-34.4% with the nAb assay. A multiplex salivary SARS-CoV-2 IgG assay demonstrated comparable performance to three commercially-available plasma EIAs and a nAb assay, and may be a viable alternative to assist in screening CCP donors and monitoring population-based seroprevalence and vaccine antibody response.
Language impairment in motor neuron disease phenotypes different from classical amyotrophic lateral sclerosis: a review

ABSTRACT Up to 35–40% of patients with amyotrophic lateral sclerosis (ALS) present with language deficits falling within the spectrum of frontotemporal lobar degeneration (FTLD). It is currently debated whether frontotemporal involvement occurs or not in motor neuron disease (MND) phenotypes that differ from classical ALS (i.e., both different-from-ALS MNDs and non-classical ALS endo-phenotypes) – this stance being supported by the notion of a common pathology underlying MNDs. To investigate whether language dysfunctions also occur in patients with different-from-classical-ALS adult-onset MNDs can; a) help determine whether the MND-FTLD continuum could be broadened at a neuropsychological level; b) convey relevant entailments to cognitive diagnostics in these populations. The present study thus aimed at reviewing evidence regarding language impairment in different-from-classical-ALS MND patients. Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were consulted to implement and report the present review. Studies were included if a) language was quantitatively assessed b) in patients diagnosed with different-from-classical-ALS MND phenotypes. Studies assessing demented patients only were excluded. From an original N = 1117 contributions, N = 20 group studies were finally included. Secondary outcomes were taken into account for qualitatively assessing potential biases in generalizing results. Studies were divided into those assessing predominant/pure-upper vs. -lower MND patients (UMND/LMND). Language dysfunctions appeared to be more prevalent and severe in UMND patients. Language screeners were able to detect language deficits in both groups. Lexical-semantic deficits appeared to be highly prevalent in both groups and a selective difficulty in action- vs. object-naming was not infrequently detected. Morpho-syntactic deficits were seldom reported in both groups. Phonological deficits and central dysgraphic features were found in UMND patients only. Patients with different-from-classical-ALS MND phenotypes display language deficits similar to those of classical ALS patients (as far as both prevalence and type are concerned) and thus could be validly included in the MND-FTLD continuum at a neuropsychological level. A greater cortical involvement might account for language deficits being more severe in UMND patients. Consistently with guidelines for cognitive assessment in ALS patients, action-naming tasks might represent a valid and sensitive tool for assessing language in UMND/LMND patients too.
Persistent COVID-19 Symptoms Minimally Impact the Development of SARS-CoV-2-Specific T Cell Immunity

SARS-CoV-2 represents an unprecedented public health challenge with many unknowns remaining regarding the factors that impact viral pathogenicity and the development of immunity after infection. While the majority of SARS-CoV-2 infected individuals with mild-to-moderate COVID-19 resolve their infection with few complications, a significant number of individuals experienced prolonged symptoms lasting for weeks after initial diagnosis. Persistent viral infections are commonly accompanied by immunologic dysregulation, especially within the cellular immune compartment. However, it is unclear if persistent mild-to-moderate COVID-19 impacts the development of virus-specific cellular immunity. To this end, we analyzed the development of SARS-CoV-2 specific cellular immunity in convalescent COVID-19 patients who experienced eight days or fewer of COVID-19 symptoms, or symptoms persisting for 18 days or more. We observed that the duration of COVID-19 symptoms minimally impacts the magnitude, antigen specificity, and transcriptional profile of SARS-CoV-2 specific cellular immunity within both the CD4+ and CD8+ T cell compartments. Furthermore, we observed that reactivity against the structural N protein from SARS-CoV-2 in convalescent COVID-19 patients correlates with the amount of reactivity against the seasonal human coronaviruses 229E and NL63. These results provide additional insight into the complex processes that regulate the development of cellular immunity against SARS-CoV-2 and related human coronaviruses
Updated SARS‐CoV‐2 single nucleotide variants and mortality association

By analyzing newly collected SARS‐CoV‐2 genomes and comparing them with our previous study about SARS‐CoV‐2 single nucleotide variants (SNVs) before June 2020, we found that the SNV clustering had changed remarkably since June 2020. Apart from that the group of SNVs became dominant, which is represented by two nonsynonymous mutations A23403G (S:D614G) and C14408T (ORF1ab:P4715L), a few emerging groups of SNVs were recognized with sharply increased monthly incidence ratios of up to 70% in November 2020. Further investigation revealed sets of SNVs specific to patients' ages and/or gender, or strongly associated with mortality. Our logistic regression model explored features contributing to mortality status, including three critical SNVs, G25088T(S:V1176F), T27484C (ORF7a:L31L), and T25A (upstream of ORF1ab), ages above 40 years old, and the male gender. The protein structure analysis indicated that the emerging subgroups of nonsynonymous SNVs and the mortality‐related ones were located on the protein surface area. The clashes in protein structure introduced by these mutations might in turn affect the viral pathogenesis through the alteration of protein conformation, leading to a difference in transmission and virulence. Particularly, we explored the fact that nonsynonymous SNVs tended to occur in intrinsic disordered regions of Spike and ORF1ab to significantly increase hydrophobicity, suggesting a potential role in the change of protein folding related to immune evasion.
Single-Blind and Double-Blind Peer Review: Effects on National Representation

ABSTRACT Purpose To assess whether the type of peer-review (single-blinded vs double-blinded) has an impact on nationality representation in journals. Methods A cross-sectional study analyzing the top 10 nationalities contributing to the number of articles across 16 ophthalmology journals. Results There was no difference in the percentage of articles published from the journal’s country of origin between the top single-blind journals and double-blind journals (SB = 42.0%, DB = 26.6%, p = .49), but there was a significant difference between the percentage of articles from the US (SB = 48.0%, DB = 22.8%, p = .02). However, there was no difference for both country of origin (SB = 38.0%, DB = 26.6%, p = .43) and articles from the US (SB = 35.0%, DB = 22.8%, p = .21) when assessing the top eight double-blind journals matched with single-blind journals of a similar impact factor. The US (n = 16, 100%) and England (n = 16, 100%) most commonly made the top 10 lists for article contribution. This held true even for journals established outside the United States (US=11/12, England = 11/12). Conclusions There was no significant difference in country-of-origin representation between single-blind journals and double-blind journals. However, higher income countries contributed most often to the journals studied even among journals based outside the US.