Miracle-dz/UniFAR-FTUs huggingface dataset:
mRNA initiation and termination are spatially coordinated

The expression of a precise mRNA transcriptome is crucial for establishing cell identity and function, with dozens of alternative isoforms produced for a single gene sequence. The regulation of mRNA isoform usage occurs by the coordination of co-transcriptional mRNA processing mechanisms across a gene. Decisions involved in mRNA initiation and termination underlie the largest extent of mRNA isoform diversity, but little is known about any relationships between decisions at both ends of mRNA molecules. Here, we systematically profile the joint usage of mRNA transcription start sites (TSSs) and polyadenylation sites (PASs) across tissues and species. Using both short and long read RNA-seq data, we observe that mRNAs preferentially using upstream TSSs also tend to use upstream PASs, and congruently, the usage of downstream sites is similarly paired. This observation suggests that mRNA 5’ end choice may directly influence mRNA 3’ ends. Our results suggest a novel “Positional Initiation-Termination Axis” (PITA), in which the usage of alternative terminal sites are coupled based on the order in which they appear in the genome. PITA isoforms are more likely to encode alternative protein domains and use conserved sites. PITA is strongly associated with the length of genomic features, such that PITA is enriched in longer genes with more area devoted to regions that regulate alternative 5’ or 3’ ends. Strikingly, we found that PITA genes are more likely than non-PITA genes to have multiple, overlapping chromatin structural domains related to pairing of ordinally coupled start and end sites. In turn, PITA coupling is also associated with fast RNA Polymerase II (RNAPII) trafficking across these long gene regions. Our findings indicate that a combination of spatial and kinetic mechanisms couple transcription initiation and mRNA 3’ end decisions based on ordinal position to define the expression mRNA isoforms.
A GPU-Accelerated Modern Fortran Version of the ECHO Code for Relativistic Magnetohydrodynamics

The numerical study of relativistic magnetohydrodynamics (MHD) plays a crucial role in high-energy astrophysics but unfortunately is computationally demanding, given the complex physics involved (high Lorentz factor flows, extreme magnetization, and curved spacetimes near compact objects) and the large variety of spatial scales needed to resolve turbulent motions. A great benefit comes from the porting of existing codes running on standard processors to GPU-based platforms. However, this usually requires a drastic rewriting of the original code, the use of specific languages like CUDA, and a complex analysis of data management and optimization of parallel processes. Here, we describe the porting of the ECHO code for special and general relativistic MHD to accelerated devices, simply based on native Fortran language built-in constructs, especially do concurrent loops, few OpenACC directives, and straightforward data management provided by the Unified Memory option of NVIDIA compilers. Thanks to these very minor modifications to the original code, the new version of ECHO runs at least 16 times faster on GPU platforms as compared to CPU-based ones. The chosen benchmark is the 3D propagation of a relativistic MHD Alfvén wave, for which strong and weak scaling tests performed on the LEONARDO pre-exascale supercomputer at CINECA are provided (using up to 256 nodes corresponding to 1024 GPUs, and over 14 billion cells). Finally, an example of high-resolution relativistic MHD Alfvénic turbulence simulation is shown, demonstrating the potential for astrophysical plasmas of the new GPU-based version of ECHO.
Blood-based targeted metabolipidomics reveals altered omega fatty acid-derived lipid mediators in relapsing-remitting multiple sclerosis patients

Unresolved and uncontrolled inflammation is considered a hallmark of pathogenesis in chronic inflammatory diseases like multiple sclerosis (MS), suggesting a defective resolution process. Inflammatory resolution is an active process partially mediated by endogenous metabolites of dietary polyunsaturated fatty acids (PUFA), collectively termed specialized pro-resolving lipid mediators (SPMs). Altered levels of resolution mediators have been reported in several inflammatory diseases and may partly explain impaired inflammatory resolution. Performing LC-MS/MS-based targeted lipid mediator profiling, we observed distinct changes in fatty acid metabolites in serum from 30 relapsing-remitting MS (RRMS) patients relative to 30 matched healthy subjects (HS). Robust linear regression revealed 12 altered lipid mediators after adjusting for confounders (p <0.05). Of these, 15d-PGJ2, PGE3, and LTB5 were increased in MS while PGF2a, 8,9-DiHETrE, 5,6-DiHETrE, 20-HETE, 15-HETE, 12-HETE, 12-HEPE, 14-HDoHE, and DHEA were decreased in MS compared to HS. In addition, 12,13-DiHOME and 12,13-DiHODE were positively correlated with expanded disability status scale values (EDSS). Using Partial Least Squares, we identified several lipid mediators with high VIP scores (VIP > 1: 32% - 52%) of which POEA, PGE3, DHEA, LTB5, and 12-HETE were top predictors for distinguishing between RRMS and HS (AUC =0.75) based on the XGBoost Classifier algorithm. Collectively, these findings suggest an imbalance between inflammation and resolution. Altogether, lipid mediators appear to have potential as diagnostic and prognostic biomarkers for RRMS.
ST and TS as Product and Sum

The set of $\mathsf{ST}$-valid inferences is neither the intersection, nor the union of the sets of $\mathsf{K}_3$- and $\mathsf{LP}$-valid inferences, but despite the proximity to both systems, an extensional characterization of $\mathsf{ST}$ in terms of a natural set-theoretic operation on the sets of $\mathsf{K}_3$- and $\mathsf{LP}$-valid inferences is still wanting. In this paper, we show that it is their relational product. Similarly, we prove that the set of $\mathsf{TS}$-valid inferences can be identified using a dual notion, namely as the relational sum of the sets of $\mathsf{LP}$- and $\mathsf{K}_3$-valid inferences. We discuss links between these results and the interpolation property of classical logic. We also use those results to revisit the duality between $\mathsf{ST}$ and $\mathsf{TS}$. We present a combined notion of duality on which $\mathsf{ST}$ and $\mathsf{TS}$ are dual in exactly the same sense in which $\mathsf{LP}$ and $\mathsf{K}_3$ are dual to each other.
Improved curvature conditions on $L^2\times\cdots\times L^2 \to L^{2/m}$ bounds for multilinear maximal averages

In this article, we focus on $L^{2}(\mathbb{R}^d)\times\cdots\times L^{2}(\mathbb{R}^d)\rightarrow L^{2/m}(\mathbb{R}^d)$ estimates for multilinear maximal averages over non-degenerate hypersurfaces. Our findings is new for $m$-linear averages with $m\geq3$, and represent a reproof of the recent result of T. Borges, B. Foster, and Y. Ou on the curvature conditions of the hypersurfaces required in establishing $L^{2}(\mathbb{R}^d)\times L^{2}(\mathbb{R}^d)\rightarrow L^{1}(\mathbb{R}^d)$ estimates of bilinear maximal functions.
Unbending combined with dehydration embrittlement as a cause for double and triple seismic zones

Using a model of elastic‐perfectly plastic plate, I demonstrate that plate unbending combined with dehydration embrittlement can account for the morphology and stresses of double or triple seismic zones (DSZ's or TSZ's) observed in many subducting slabs. Densifying metamorphic reactions may induce tensile stresses as well as high pore fluid pressures in the slab crust and thus generate the upper seismicity band of the TSZ. Limited dehydration may moderately elevate the fluid pressure in the slab mantle, but unbending usually dominates mantle stresses and results in another two seismicity bands. DSZ's are underdeveloped TSZ's.
A topological description of loss surfaces based on Betti Numbers

In the context of deep learning models, attention has recently been paid to studying the surface of the loss function in order to better understand training with methods based on gradient descent. This search for an appropriate description, both analytical and topological, has led to numerous efforts to identify spurious minima and characterize gradient dynamics. Our work aims to contribute to this field by providing a topological measure to evaluate loss complexity in the case of multilayer neural networks. We compare deep and shallow architectures with common sigmoidal activation functions by deriving upper and lower bounds on the complexity of their loss function and revealing how that complexity is influenced by the number of hidden units, training models, and the activation function used. Additionally, we found that certain variations in the loss function or model architecture, such as adding an $\ell_2$ regularization term or implementing skip connections in a feedforward network, do not affect loss topology in specific cases.
CAPTAIN at COLIEE 2023: Efficient Methods for Legal Information Retrieval and Entailment Tasks

The Competition on Legal Information Extraction/Entailment (COLIEE) is held annually to encourage advancements in the automatic processing of legal texts. Processing legal documents is challenging due to the intricate structure and meaning of legal language. In this paper, we outline our strategies for tackling Task 2, Task 3, and Task 4 in the COLIEE 2023 competition. Our approach involved utilizing appropriate state-of-the-art deep learning methods, designing methods based on domain characteristics observation, and applying meticulous engineering practices and methodologies to the competition. As a result, our performance in these tasks has been outstanding, with first places in Task 2 and Task 3, and promising results in Task 4. Our source code is available at https://github.com/Nguyen2015/CAPTAIN-COLIEE2023/tree/coliee2023.
Structured factor copulas for modeling the systemic risk of European and United States banks (preprint)

In this paper, we employ Credit Default Swaps (CDS) to model the joint and conditional distress probabilities of banks in Europe and the U.S. using factor copulas. We propose multi-factor, structured factor, and factor-vine models where the banks in the sample are clustered according to their geographic location. We find that within each region, the co-dependence between banks is best described using both, systematic and idiosyncratic, financial contagion channels. However, if we consider the banking system as a whole, then the systematic contagion channel prevails, meaning that the distress probabilities are driven by a latent global factor and region-specific factors. In all cases, the co-dependence structure of bank CDS spreads is highly correlated in the tail. The out-of-sample forecasts of several measures of systematic risk allow us to identify the periods of distress in the banking sector over the recent years including the COVID-19 pandemic, the interest rate hikes in 2022, and the banking crisis in 2023.
Evolved Massive Stars at Low Metallicity. VI. Mass-loss Rate of Red Supergiant Stars in the Large Magellanic Cloud

Mass loss is a crucial process that affects the observational properties, evolution path, and fate of highly evolved stars. However, the mechanism of mass loss is still unclear, and the mass-loss rate (MLR) of red supergiant stars (RSGs) requires further research and precise evaluation. To address this, we utilized an updated and complete sample of RSGs in the Large Magellanic Cloud (LMC) and employed the 2-DUST radiation transfer model and spectral energy distribution fitting approach to determine the dust-production rates (DPRs) and dust properties of the RSGs. We have fitted 4714 selected RSGs with over 100,000 theoretical templates of evolved stars. Our results show that the DPR range of RSGs in the LMC is 10−11 M ⊙ yr−1–10−7 M ⊙ yr−1, and the total DPR of all RSGs is 1.14 ×10−6 M ⊙ yr−1. We find that 63.3% RSGs are oxygen-rich, and they account for 97.2% of the total DPR. The optically thin RSG, which comprise 30.6% of our sample, contribute only 0.1% of the total DPR, while carbon-rich RSGs (6.1%) produce 2.7% of the total DPR. Overall, 208 RSGs contributed 76.6% of the total DPR. We have established a new relationship between the MLR and luminosity of RSGs in the LMC, which exhibits a positive trend and a clear turning point at logL/L⊙≈4.4 .
Giant Outer Transiting Exoplanet Mass (GOT ‘EM) Survey. IV. Long-term Doppler Spectroscopy for 11 Stars Thought to Host Cool Giant Exoplanets

Discovering and characterizing exoplanets at the outer edge of the transit method’s sensitivity has proven challenging owing to geometric biases and the practical difficulties associated with acquiring long observational baselines. Nonetheless, a sample of giant exoplanets on orbits longer than 100 days has been identified by transit hunting missions. We present long-term Doppler spectroscopy for 11 such systems with observation baselines spanning a few years to a decade. We model these radial velocity observations jointly with transit photometry to provide initial characterizations of these objects and the systems in which they exist. Specifically, we make new precise mass measurements for four long-period giant exoplanets (Kepler-111 c, Kepler-553 c, Kepler-849 b, and PH-2 b), we place new upper limits on mass for four others (Kepler-421 b, KOI-1431.01, Kepler-1513 b, and Kepler-952 b), and we show that several confirmed planets are in fact not planetary at all. We present these findings to complement similar efforts focused on closer-in short-period giant planets, and with the hope of inspiring future dedicated studies of cool giant exoplanets.
Distribution features of nutrients and flux across the sediment-water interface in the Sanggou Bay

Four cruises are conducted in the Sanggou Bay in April,July,November 2006 and January 2007,nutrient distributions,structure features,primary control processes and exchange fluxes across the sediment-water interface are dscussed.The results indicate that nutrient concentrations show obvious seasonal changes.The concentrations of NO-3,NO-2,PO3-4,DOP,TDP and SiO2-3are the highest in autumn,while the concentrations of NH+4-N,DON and TDN show the highest in summer.The concentrations of nutrients are the lowest in spring except DON.In spring,the water exchange between the Sanggou Bay and the Huanghai Sea and the uptake by large phytoplankton result in the concentrations of nutrients at lower level in the bay.In summer and autumn,the riverine input affects the nutrient levels.In winter,the nutrient levels are affected by coastal waters.The structure of P shows a more obvious change and DOP is the major component in summer which can be 81%. The structure of N transforms from DON to DIN domination.The atom ratio of Si to N changes slightly in the whole year,while the atom ratios of Si to N and N to P in spring and summer are higher those that in autumn and winter.Based on the analysis of nutrient limiting criterion and the lowest threshold values of the phytoplankton growth,P is the limiting factor for the phytoplankton growth in spring and summer in the Sanggou Bay.Si is also a potential limiting factor in spring with the concentration lower than the threshold value of the phytoplankton growth,which shows that the contributions of NH+4,PO3-4 and SiO2-3fluxes released from the sediment to primary production is quite limited.Comparing to other shallow sea environments,the benthic nutrient fluxes in the Sanggou Bay are ranked at the lower level.
Structure Inducing Pre-Training

We present a theoretical analysis from first principles that establishes a novel connection between relational inductive bias of pre-training and fine-tuning performance while providing an extended view on general pre-training models. We further explore how existing pretraining methods impose relational inductive biases, finding that the vast majority of existing approaches focus almost exclusively on modelling relationships in an intra-sample manner, rather than a per-sample manner. We build upon these findings with simulations and empirical studies on standard benchmarks spanning 3 data modalities and 10 downstream tasks. These investigations validate our theoretical analyses, and provides a recipe to produce new pre-training methods which incorporate provably richer inductive biases than do existing methods in line with user specified relational graphs.
Comparison of NOAA AVHRR Data to Meteorologic Drought Indices

Evaluation of the AVHRR sensor on-board the NOAA-6 satellite shows that the spatial and temporal variations in drought conditions as defined by the Crop Moisture Index (CMI), Drought Severity Index (DSI), and the Hydrologic Deficit (HD) can be estimated by a combination of remote sensing vegetation indices. Multiple regression analysis explains 80, 57, and 44 percent of the variation in the CMI, DSI, and the HD, respectively, when regressed against AVHRR spectral channels and derived vegetation indices for four study periods extending from June through August, 1980. Regression R2 values for a single selected study period range from 62 to 90 percent, 68 to 91 percent, and 51 to 88 percent of the variation in each of the nine Oklahoma climatic divisions for the SMI, DSI and the HD, respectively.
Parasitos intestinais em galinhas caipiras da região metropolitana de Porto Alegre, RS

The aim of this study was to determine the prevalence of intestinal parasites in free range chicken reared in extensive conditions in the metropolitan region of Porto Alegre. 112 fecal specimens were analyzed poultry properties 14 and processed by flotation techniques with saturated solution of sodium chloride and spontaneous sedimentation. Thirteen properties (92.9 %) were parasitized birds. The overall prevalence was 55.4 % (62/112) of the infected birds with helminth eggs of genus Capillaria, Heterakis, Ascaridia, Strongyloides, Strongyloidea and protozoa of the genus Eimeria. The only cestode found was the genus Choanotaenia. Capillaria sp. was the most prevalent helminth (78.6 %) independent municipality. The parasitological diagnosis using fecal samples is suitable tool to assist in parasitic control. Although the prevalence detected was high, the creators showed no health problem in poultry.
Mediating effect of cumulative lipid pro�le burden on the effect of diet and obesity on hypertension incidence: a cohort study of people aged 35-65 in rural China

Cumulative lipid pro�le burden is designed to dynamically measure lipid accumulation, and its effect on hypertension has been poorly studied. Our main purpose was to investigate the effect of cumulative lipid pro�le burden on the incidence of essential hypertension (EH) and. Secondly, to investigate whether there is a mediating role of cumulative lipid burden in the pathogenesis of the effects of diet and obesity on EH. A total of 1 295 participants were included in the study, which began in 2017. The average follow-up time was 2.98 years. A total of 240 EH patients occurred during the follow-up period. Compared with respective reference groups, the HR (95% CI) of the highest quartile in cumulative TC, TG and HDL burden were 1.747 (1.145 - 2.664), 1.502 (1.038 - 2.173), 0.615 (0.413 - 0.917) for incidence of EH. Participants with EH consumed more red meat and re�ned grains, and red meat was positively associated with cumulative TC burden . BMI and Waist-To-Height Ratio (WHtR) increased the incidence of EH, and obesity was positively correlated with cumulative TC burden. cumulative TC burden play a partially mediating role in the in�uence of obesity on EH ( β indirect =0.0085, 95%CI: 0.0035, 0.1520). The cumulation TG, TC burden increased the risk of EH, while the cumulation HDL reduced the risk of EH. cumulative TG burden play a partially mediating role in the in�uence of obesity on EH. Diet was not found to in�uence hypertension through cumulative lipid pro�le burden.
2022 Asymptotic distributions of the number of zeros of random polynomials in Hayes equivalence class over a ﬁnite ﬁeld

Hayes equivalence is deﬁned on monic polynomials over a ﬁnite ﬁeld F q in terms of the prescribed leading coeﬃcients and the residue classes modulo a given monic polynomial Q . We study the distribution of the number of zeros in a random polynomial over ﬁnite ﬁelds in a given Hayes equivalence class. It is well known that the number of distinct zeros of a random polynomial over F q is asymptotically Poisson with mean 1. We show that this is also true for polynomials in any given Hayes equivalence class. Asymptotic formulas are also given for the number of such polynomials when the degree of Q and the number of prescribed leading coeﬃcients are relatively small. When the equivalence class is deﬁned by leading coeﬃcients only, the problem is equivalent to the study of the distance distribution in Reed-Solomon codes and our asymptotic formulas extend some earlier results.
The Relationship between the Brain-Derived Neurotrophic Factor Gene Polymorphism (Val66Met) and Substance Use Disorder and Relapse

Substance addiction is a neuropsychiatric disorder characterized by a recurring desire to continue using a substance despite harmful consequences. Brain-derived neurotrophic factor (BDNF) is a protein that plays a role in the activity-dependent remodeling of neural function in adult nervous systems. This study analyzed the association of the rs6265 polymorphism of the BDNF gene in a group of patients addicted to psychoactive substances who were participating in addiction treatment for the first time, in a group of post-relapse psychoactive substance abusers and in a control group. The study also assessed personality and anxiety in all study groups. Statistically significant differences in the frequency of genotypes and alleles were found between all study groups. Compared to the control, both study groups had statistically significantly higher scores for trait and state anxiety. Addicted patients in both groups also had higher scores on the Neuroticism and Openness scales and lower scores on the Extraversion and Agreeableness scales. The results of this study provide further evidence that personality traits, anxiety and the rs6265 polymorphism of the BDNF gene may be risk factors for susceptibility to addiction to psychoactive substances. In addition, they can be a predictor of addiction relapse, but further extensive studies are required to confirm these findings.
Genomic Insights into the Population History and Adaptive Traits of 1 Latin American Criollo Cattle

28 Criollo cattle, descendants of animals brought by Iberian colonists to the Americas, have been 29 subject to centuries of natural and human-mediated selection in novel tropical agroecological zones. 30 Consequently, these breeds have evolved distinct characteristics such as resistance to disease and 31 exceptional heat tolerance. In addition to European taurine ( Bos taurus ) ancestry, it has been 32 proposed that gene flow from African taurine and Asian zebu ( Bos indicus ) cattle has shaped the 33 ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela 34 using whole genome sequencing data to examine population structure and admixture at very high 35 resolution. We did not detect evidence of African taurine admixture in Criollo cattle; however, there 36 was evidence of longstanding zebu ancestry in one breed (Hartón del Valle). In addition, we 37 detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to 38 thermotolerance, reproduction, fertility, immunity, and distinct coat and skin coloration traits. This 39 study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness 40 and potential of these breeds in the face of climate change, habitat flux, and disease challenges. 41 Further research is warranted to leverage these findings for more effective and sustainable cattle 42 breeding programmes. 43