Miracle-dz/UniFAR-FTUs huggingface dataset:
Shared genetic mechanism between type 2 diabetes and COVID-19 using pathway-based association analysis

Recent studies have shown that, compared with healthy individuals, patients with type 2 diabetes (T2D) suffer a higher severity and mortality of COVID-19. When infected with this retrovirus, patients with T2D are more likely to face severe complications from cytokine storms and be admitted to high-dependency or intensive care units. Some COVID-19 patients are known to suffer from various forms of acute respiratory distress syndrome and have a higher mortality risk due to extreme activation of inflammatory cascades. Using a conditional false discovery rate statistical framework, an independent genome-wide association study data on individuals presenting with T2D (N = 62,892) and COVID-19 (N = 38,984) were analysed. Genome-wide association study data from 2,343,084 participants were analysed and a significant positive genetic correlation between T2D and COVID-19 was observed (T2D: r for genetic = 0.1511, p-value = 0.01). Overall, 2 SNPs (rs505922 and rs3924604) shared in common between T2D and COVID-19 were identified. Functional analyses indicated that the overlapping loci annotated into the ABO and NUS1 genes might be implicated in several key metabolic pathways. A pathway association analysis identified two common pathways within T2D and COVID-19 pathogenesis, including chemokines and their respective receptors. The gene identified from the pathway analysis (CCR2) was also found to be highly expressed in blood tissue via the GTEx database. To conclude, this study reveals that certain chemokines and their receptors, which are directly involved in the genesis of cytokine storms, may lead to exacerbated hyperinflammation in T2D patients infected by COVID-19.
Gut microbiota alterations may increase the risk of prescription opioid use, but not vice versa: A two-sample bi-directional Mendelian randomization study

Introduction Gut microbiota alterations are strongly associated with prescription opioid use (POU) and multisite chronic pain (MCP). However, whether or not these associations are causal remains unknown. Therefore, we aim to explore the causal relationships between them comprehensively. Methods A two-sample bi-directional Mendelian randomization was conducted to assess the potential associations between gut microbiota and POU/MCP using summary level Genome-wide association studies (GWASs) that were based on predominantly European ancestry. Results Potential causal effects were identified between seven host genetic-driven traits of gut microbiota on POU, including Adlercreutzia, Allisonella, Dialister, Anaerofilum, Anaerostipes, ChristensenellaceaeR.7group, and LachnospiraceaeNC2004group at the genus level (p < 0.05) by the Inverse-variance weighted method, with significant causal effects of ChristensenellaceaeR.7group and Allisonella on POU (p < 0.025). A total of five genetically greater abundance of gut microbiota traits were identified to be possibly related to the level of MCP (p < 0.05), including genus ErysipelotrichaceaeUCG003, family Clostridiaceae1, order Gastranaerophilales, order Actinomycetales, and family Actinomycetaceae. In the other direction, no clear evidence was found to support a significant causal relationship between POU and gut microbiota, as well as MCP and gut microbiota. In addition, evidence was also provided for the relationship between triacylglycerols and diacylglycerol elevation, and an increased risk of POU and MCP. No evidence was found across various sensitivity analyses, including reverse causality, pleiotropy, and heterogeneity. Conclusion The findings from this study provide robust evidence that gut microbiota alterations may be a risk of POU/MCP, but not vice versa.
Association between socioeconomic status and arteriosclerotic cardiovascular disease risk and cause-specific and all-cause mortality: Data from the 2005–2018 National Health and Nutrition Examination Survey

Background Morbidity and mortality of arteriosclerotic cardiovascular disease (ASCVD) varied according to socioeconomic status (SES), and evidence on the association between SES and ASCVD risk, and cause-specific and all-cause mortality was nevertheless lacking in large-scale or population-based studies. Methods A multicycle cross-sectional design and mortality linkage study was conducted using data from Continuous National Health and Nutrition Examination Survey (NHANES) in the United States, including public use linked mortality follow-up files through December 31, 2019. Poverty income ratio (PIR) served as a SES index. A series of weighted Logistic regressions and Cox proportional hazards regressions were used to investigate the association between the SES and the risk of ASCVD and mortality, respectively. Results The study sample was comprised of 30,040 participants aged 20–85 years old during the 2005–2018 period. Weighted Logistic regression models consistently indicated significant relationship between people experiencing poverty and increased risk of ASCVD, and linear trend tests were all statistically significant (all P for trend < 0.001). Additionally, weighted Cox regression analysis consistently demonstrated that the hazards of cause-specific and all-cause mortality increased, with the decrease of each additional income level, and trend analyses indicated similar results (all P for trend < 0.001). Conclusions Our study confirmed that the SES was strongly linked to living with ASCVD, and cause-specific and all-cause mortality, even after adjusting for other factors that could impact risk, such as the American Heart Association (AHA)'s Life's Simple 7 cardiovascular health score and variables of age, sex, marital status, education, and depression severity.
Remarks on Syzygies of the Section Modules and Geometry of Projective Varieties

Let X ⊂ ℙ(H 0(ℒ)) be a smooth projective variety embedded by the complete linear system associated to a very ample line bundle ℒ on X. We call the section module of ℒ. It has been known that the syzygies of R ℒ as R = Sym(H 0(ℒ))-module play important roles in understanding geometric properties of X [2, 3, 5, 9, 10] even if X is not projectively normal. Generalizing the case of N 2, p [2, 10], we prove some uniform theorems on higher normality and syzygies of a given linearly normal variety X and general inner projections when R ℒ satisfies property N 3, p (Theorems 1.1, 1.2, and Proposition 3.1). In particular, our uniform bounds are sharp as hyperelliptic curves and elementary transforms of elliptic ruled surfaces show.
A note on Lang's conjecture for quotients of bounded domains

It was conjectured by Lang that a complex projective manifold is Kobayashi hyperbolic if and only if it is of general type together with all of its subvarieties. We verify this conjecture for projective manifolds whose universal cover carries a bounded, strictly plurisubharmonic function. This includes in particular compact free quotients of bounded domains. Comment: 10 pages, no figures, comments are welcome. v3: following suggestions made by the referee, the exposition has been improved all along the paper, we added a variant of Theorem A which includes manifolds whose universal cover admits a bounded psh function which is strictly psh just at one point, and we added a section of examples. Final version, to appear on \'Epijournal G\'eom. Alg\'ebrique
Affine motion of 2d incompressible fluids and flows in ${\rm SL}(2,{\mathbb R})$

The affine motion of two-dimensional (2d) incompressible fluids can be reduced to a completely integrable and globally solvable Hamiltonian system of ordinary differential equations for the deformation gradient in ${\rm SL}(2,{\mathbb R})$. In the case of perfect fluids, the motion is given by geodesic flow in ${\rm SL}(2,{\mathbb R})$ with the Euclidean metric, while for magnetically conducting fluids (MHD), the motion is governed by a harmonic oscillator in ${\rm SL}(2,{\mathbb R})$. A complete description of the dynamics is given including rigid motions, rotating eddies with stable and unstable manifolds, and solutions with vanishing pressure. For perfect fluids, the displacement generically becomes unbounded, as $t\to\pm\infty$. For MHD, solutions are bounded and generically multiply periodic and recurrent.
A framework for non-asymptotic quantum information theory

This thesis consolidates, improves and extends the smooth entropy framework for non-asymptotic information theory and cryptography. We investigate the conditional min- and max-entropy for quantum states, generalizations of classical R\'enyi entropies. We introduce the purified distance, a novel metric for unnormalized quantum states and use it to define smooth entropies as optimizations of the min- and max-entropies over a ball of close states. We explore various properties of these entropies, including data-processing inequalities, chain rules and their classical limits. The most important property is an entropic formulation of the asymptotic equipartition property, which implies that the smooth entropies converge to the von Neumann entropy in the limit of many independent copies. The smooth entropies also satisfy duality and entropic uncertainty relations that provide limits on the power of two different observers to predict the outcome of a measurement on a quantum system. Finally, we discuss three example applications of the smooth entropy framework. We show a strong converse statement for source coding with quantum side information, characterize randomness extraction against quantum side information and prove information theoretic security of quantum key distribution using an intuitive argument based on the entropic uncertainty relation.
Flexible pH sensors based on polysilicon thin film transistors and ZnO nanowalls

A fully flexible pH sensor using nanoporous ZnO on extended gate thin film transistor (EGTFT) fabricated on polymeric substrate is demonstrated. The sensor adopts the Low Temperature Polycrystalline Silicon (LTPS) TFT technology for the active device, since it allows excellent electrical characteristics and good stability and opens the way towards the possibility of exploiting CMOS architectures in the future. The nanoporous ZnO sensitive film, consisting of very thin (20 nm) crystalline ZnO walls with a large surface-to-volume ratio, was chemically deposited at 90 °C, allowing simple process integration with conventional TFT micro-fabrication processes compatible with wide range of polymeric substrates. The pH sensor showed a near-ideal Nernstian response (∼59 mV/pH), indicating an ideality factor α ∼ 1 according to the conventional site binding model. The present results can pave the way to advanced flexible sensing systems, where sensors and local signal conditioning circuits will be integrated on the same flexible substrate.
Fukaya categories of Lagrangian cobordisms and duality

We introduce a new type of duality structure for $A_\infty$-categories called a relative weak Calabi-Yau pairing which generalizes Kontsevich and Soibelman's notion of a weak (proper) Calabi-Yau structure. We prove the existence of a relative weak Calabi-Yau pairing on Biran and Cornea's Fukaya category of Lagrangian cobordisms $\mathcal{F}uk_{\mathit{cob}}(\mathbb{C}\times M)$. Here $M$ is a symplectic manifold which is closed or tame at infinity. This duality structure on $\mathcal{F}uk_{\mathit{cob}}(\mathbb{C}\times M)$ extends the relative Poincare duality satisfied by Floer complexes for pairs of Lagrangian cobordisms. Moreover, we show that the relative weak Calabi-Yau pairing on $\mathcal{F}uk_{\mathit{cob}}(\mathbb{C}\times M)$ satisfies a compatibility condition with respect to the usual weak Calabi-Yau structure on the monotone Fukaya category of $M$. The construction of the relative weak Calabi-Yau pairing on $\mathcal{F}uk_{\mathit{cob}}(\mathbb{C}\times M)$ is based on counts of curves in $\mathbb{C}\times M$ satisfying an inhomogeneous nonlinear Cauchy-Riemann equation. In order to prove the existence of this duality structure and to verify its properties, we extend the methods of Biran and Cornea to establish regularity and compactness results for the relevant moduli spaces. We also consider the implications of the existence of the relative weak Calabi-Yau pairing on $\mathcal{F}uk_{\mathit{cob}}(\mathbb{C}\times M)$ for the cone decomposition in the derived Fukaya category of $M$ associated to a Lagrangian cobordism, and we present an example involving Lagrangian surgery.
Normal approximation of the solution to the stochastic wave equation with L\'evy noise

For a sequence $\dot{L}^{\varepsilon}$ of L\'evy noises with variance $\sigma^2(\varepsilon)$, we prove the Gaussian approximation of the solution $u^{\varepsilon}$ to the stochastic wave equation driven by $\sigma^{-1}(\varepsilon) \dot{L}^{\varepsilon}$ and thus extend the result of C. Chong and T. Delerue [Stoch. Partial Differ. Equ. Anal. Comput. (2019)] to the class of hyperbolic stochastic PDEs. That is, we find a necessary and sufficient condition in terms of $\sigma^2(\varepsilon)$ for $u^{\varepsilon}$ to converge in law to the solution to the same equation with Gaussian noise. Furthermore, $u^{\varepsilon}$ is shown to have a space-time version with a c\`adl\`ag property determined by the wave kernel, and its derivative $\partial_t u^{\varepsilon}$ a c\`adl\`ag version when viewed as a distribution-valued process. These two path properties are essential to our proof of the normal approximation as the limit is characterized by martingale problems that necessitate both random elements. Our results apply to additive as well as to multiplicative noises.
Multistring vertices and hyperbolic Kac-Moody algebras

Multistring vertices and the overlap identities which they satisfy are exploited to understand properties of hyperbolic Kac-Moody algebras, in particular E10. Since any such algebra can be embedded in the larger Lie algebra of physical states of an associated completely compactified subcritical bosonic string, one can in principle determine the root spaces by analyzing which (positive norm) physical states decouple from the N-string vertex. Consequently, the Lie algebra of physical states decomposes into a direct sum of the hyperbolic algebra and the space of decoupled states. Both these spaces contain transversal and longitudinal states. Longitudinal decoupling holds more generally, and may also be valid for uncompactified strings, with possible consequences for Liouville theory; the identification of the decoupled states simply amounts to finding the zeroes of certain “decoupling polynomials. ” This is not the case for transversal decoupling, which crucially depends on special properties of the root lattice, as we explicitly demonstrate for a nontrivial root space of E10· Because the N-vertices of the compactified string contain the complete information about decoupling, all the properties of the hyperbolic algebra are encoded into them. In view of the integer grading of hyperbolic algebras such as E10 by the level, these algebras can be interpreted as interacting strings moving on the respective group manifolds associated with the underlying finite-dimensional Lie algebras.
Comparison of methods for harmonic wavelet analysis of heart rate variability

Two different methods for the spectral analysis of heart rate variability data are compared: the discrete Fourier transform and the nonequispaced Fourier transform. The methods are used to analyse test signals that are constructed to mimic R-R interval data, with graded levels of noise, generated using the integral pulse frequency modulation model. It is found that the nonequispaced Fourier transform is the better method for determining the frequency coefficients of the test signals as the noise level is increased. Both methods are compared when they are used as the first step in a time-frequency analysis of the test signals using the discrete harmonic wavelet transform, and a quantitative comparison is made on a set of randomly generated test signals (this shows that the nonequispaced Fourier transform is the better method). A further study shows the ability of the discrete harmonic wavelet transform to detect frequencies close to the boundary between wavelet levels. Since each harmonic wavelet represents a distinct frequency band, careful choice of sampling frequency means that such wavelets can be used to identify spectral bands associated with physiological causes. A clinical example, using the nonequispaced Fourier transform, shows how the discrete harmonic wavelet transform could be developed for use in detecting brief alterations in autonomic tone.
Asymptotic analysis of generalized Hermite polynomials

We analyze the polynomials Hnr(x) considered by Gould and Hopper, which generalize the classical Hermite polynomials. We present the main properties of Hnr(x) and derive asymptotic approximations for large values of n from their differential-difference equation, using a discrete ray method. We give numerical examples showing the accuracy of our formulas.
Serum total cholesterol level as a potential predictive biomarker for neurological outcomes in cardiac arrest survivors who underwent target temperature management

Cholesterol is an essential substance to maintain cell membranes. Low levels of total cholesterol (TC) are associated with poor prognosis in critically ill patients. Cardiac arrest-induced whole-body ischemia and reperfusion injury cause a sepsis-like syndrome. The Cholesterol level in post-cardiac arrest patients may indicate the degree of endotoxemia or inflammation caused by ischemic and reperfusion injury. We aimed to investigate the association of TC levels with neurologic outcome of out-of-hospital cardiac arrest (OHCA) survivors who underwent target temperature management (TTM). This was a retrospective single-center observational study from May 2018 to April 2021 on a cohort of 106 patients. TC levels were determined in samples obtained immediately and at 24, 48, and 72 hours after the return of spontaneous circulation (ROSC). The primary outcome was poor neurologic outcome at 3 months after ROSC. Poor neurologic outcome was defined by cerebral performance categories 3 to 5. Sixty patients had a poor neurologic outcome. TC levels were significantly lower in the poor neurologic outcome group at each time point. The TC levels for predicting poor neurologic outcome had a sensitivity of 80.8%, with 67.6% specificity at 48 hours (TC48) after ROSC. The areas under the curve value of TC48 was 0.771 (0.670–0.853), with a cutoff value of 114 mg/dL. TC level at 48 hours after ROSC was a helpful marker for the 3-month poor neurologic outcome. This might be an easily accessible predictive marker of neurologic outcome in OHCA survivors treated with TTM.
Possible association between the lrrk2 gene and anxiety behavior: a systematic literature review

Abstract Alterations to the LRRK2 gene have been associated with Parkinson’s disease and alcohol consumption in animals and humans. Furthermore, these disorders are strongly related to anxiety disorders (ADs). Thus, we investigated how the LRRK2 gene might influence anxiety in humans and mice. We elaborated a systematic review based on the PRISMA Statement of studies that investigated levels of anxiety in animal or human models with alterations in the LRRK2 gene. The search was conducted in the PubMed, Scopus, and Web of Science databases, and in reference lists with descriptors related to ADs and the LRRK2. From the 62 articles assessed for eligibility, 16 were included: 11 conducted in humans and seven, in mice. Lrrk2 KO mice and the LRRK2 G2019S, LRRK2 R1441G, and LRRK2 R1441C variants were addressed. Five articles reported an increase in anxiety levels concerning the LRRK2 variants. Decreased anxiety levels were observed in two articles, one focusing on the LRRK2 G2019S and the other, on the Lrrk2 KO mice. Eight other articles reported no differences in anxiety levels in individuals with Lrrk2 alterations compared to their healthy controls. This study discusses a possible influence between the LRRK2 gene and anxiety, adding information to the existing knowledge respecting the influence of genetics on anxiety.
Anatomical study of the red flour beetle using synchrotron radiation X‐ray phase‐contrast micro‐tomography

Synchrotron X‐ray phase‐contrast microtomography (SR‐PhC micro‐CT) is well established, fast and non‐destructive imaging technique for data acquisition that is currently being used to obtain new insights into insect anatomy and function in physiological, morphological and phylogenetic studies. In this study, we described in situ the internal organs of the red flour beetle Tribolium castaneum Herbst 1797, a widespread pest of cereals and stored food causing serious damage to the human economy. Two‐dimensional virtual sections and volumetric reconstructions of the nervous, alimentary and reproductive systems were carried out in both sexes. The results provided a comprehensive overview of the morphological characteristics of this species, such as the different maturation stages of ovarioles and the realistic location, size and shape of internal organs. Given the great interest in this model species in experimental biology and forensic entomology, complete knowledge of the general anatomy is required for future functional applications in pest control and experimental studies. In addition, this study confirms SR‐PhC micro‐CT as a powerful and innovative tool in entomology, particularly suitable for small species and chitinized structures that are difficult to analyse using conventional dissection and histological methods.
Hypercoagulability in critically ill patients with COVID 19, an observational prospective study

Objective COVID 19 is often associated with hypercoagulability and thromboembolic (TE) events. The aim of this study was to assess the characteristics of hypercoagulability and its relationship with new-onset TE events and the composite outcome of need for intubation and/or death in intensive care unit (ICU) patients admitted for COVID. Design Prospective observational study. Setting Monocentric, intensive care, University Hospital of Clermont Ferrand, France. Patients Patients admitted to intensive care from January 2020 to May 2021 for COVID-19 pneumonia. Interventions Standard hemostatic tests and rotational thromboelastometry (ROTEM) were performed on admission and on day 4. Hypercoagulability was defined by at least one of the following criteria: D-dimers > 3000 μg/dL, fibrinogen > 8 g/L, EXTEM CFT below the normal range, EXTEM A5, MCF, Li 60 above the normal range, and EXTEM G-score ((5000 x MCF) / (100-MCF)) ≥ 11 dyne/cm2. Measurements and main results Of the 133 patients included, 17 (12.7%) developed new-onset TE events, and 59 (44.3%) required intubation and/or died in the ICU. ROTEM was performed in 133 patients on day 1 and in 67 on day 4. Hypercoagulability was present on day 1 in 115 (86.4%) patients. None of the hypercoagulability indices were associated with subsequent new-onset TE events on days 1 and 4 nor with the need for intubation and/or ICU death. Hyperfibrinogenemia > 8g/dL, higher D-dimers and higher EXTEM Li 60 on day 4 were predictive of need for intubation and/or of ICU death. Conclusions Our study confirmed that most COVID-19 ICU patients have hypercoagulability on admission and almost all on day 4. Hyperfibrinogenemia or fibrinolysis shutdown on day 4 were associated with unfavorable outcome.