Miracle-dz/UniFAR-FTUs huggingface dataset:
The model logic Z applied to Lifschitz's benchmark problems for formal nonmonotonic reasoning

To give a standard against which to judge the limitations and possibilities of a theory of nonmonotonic reasoning, V. Lifschitz presented a paper at the 1988 Second International Workshop on Non-Monotonic Reasoning entitled "Benchmark Problems for Formal Nonmonotonic Reasoning. " We show in this work the application of the modal logic Z to these benchmark problems. The modal logic Z provides a consistency-based approach to nonmonotonic reasoning. Z is a fragment of second order modal quantificational logic involving quantification over propositions but not over properties. We demonstrate that Z leads to correct and concise solutions to all the benchmark problems. We also show that many solutions to nonmonotonic reasoning problems expressed in Z are automatically derivable. Because we are able to solve the benchmark problems by hand using a small number of lemmas, we claim that Z has a learnable proof theory. In addition to handling all the benchmark problems, which to our knowledge has not been demonstrated for a single system of nonmonotonic reasoning, we also make a number of smaller contributions. This work provides solutions to the unique name problems which, to our knowledge, have not been solved by any other formal system. It demonstrates a new representation in Z for temporal projection, and improves on a representation by Lifschitz for temporal explanation. It describes a way of generalizing temporal projection to handle concurrent actions, and a way of using temporal explanation for counterfactual reasoning. It shows that Z is able to reason correctly about autoepistemic problems, including problems with quantification. Finally, it reports results on our use of and extensions to a theorem prover for Z.
The Slaughterhouse as Hotspot of CC1 and CC6 Listeria monocytogenes Strains with Hypervirulent Profiles in an Integrated Poultry Chain of Italy

In Europe, very few studies are available regarding the diversity of Listeria monocytogenes (L. monocytogenes) clonal complexes (CCs) and sequence types (ST) in poultry and on the related typing of isolates using whole genome sequencing (WGS). In this study, we used a WGS approach to type 122 L. monocytogenes strains isolated from chicken neck skin samples collected in two different slaughterhouses of an integrated Italian poultry company. The studied strains were classified into five CCs: CC1-ST1 (21.3%), CC6-ST6 (22.9%), CC9-ST9 (44.2%), CC121-ST121 (10.6%) and CC193-ST193 (0.8%). CC1 and CC6 strains presented a virulence gene profile composed of 60 virulence genes and including the Listeria Pathogenicity Island 3, aut_IVb, gltA and gltB. According to cgMLST and SNPs analysis, long-term persistent clusters belonging to CC1 and CC6 were found in one of the two slaughterhouses. The reasons mediating the persistence of these CCs (up to 20 months) remain to be elucidated, and may involve the presence and the expression of stress response and environmental adaptation genes including heavy metals resistance genes (cadAC, arsBC, CsoR-copA-copZ), multidrug efflux pumps (mrpABCEF, EmrB, mepA, bmrA, bmr3, norm), cold-shock tolerance (cspD) and biofilm-formation determinants (lmo0673, lmo2504, luxS, recO). These findings indicated a serious risk of poultry finished products contamination with hypervirulent L. monocytogenes clones and raised concern for the consumer health. In addition to the AMR genes norB, mprF, lin and fosX, ubiquitous in L. monocytogenes strains, we also identified parC for quinolones, msrA for macrolides and tetA for tetracyclines. Although the phenotypical expression of these AMR genes was not tested, none of them is known to confer resistance to the primary antibiotics used to treat listeriosis The obtained results increase the data on the L. monocytogenes clones circulating in Italy and in particular in the poultry chain.
Dietary Docosahexaenoic Acid and Glucose Systemic Metabolic Changes in the Mouse

The endocannabinoid system (ECS) participates in regulating whole body energy balance. Overactivation of the ECS has been associated with the negative consequence of obesity and type 2 diabetes. Since activators of the ECS rely on lipid-derived ligands, an investigation was conducted to determine whether dietary PUFA could influence the ECS to affect glucose clearance by measuring metabolites of macronutrient metabolism. C57/blk6 mice were fed a control or DHA-enriched semi-purified diet for a period of 112 d. Plasma, skeletal muscle, and liver were collected after 56 d and 112 d of feeding the diets for metabolomics analysis. Key findings characterized a shift in glucose metabolism and greater catabolism of fatty acids in mice fed the DHA diet. Glucose use and promotion of fatty acids as substrate were found based on levels of metabolic pathway intermediates and altered metabolic changes related to pathway flux with DHA feeding. Greater levels of DHA-derived glycerol lipids were found subsequently leading to the decrease of arachidonate-derived endocannabinoids (eCB). Levels of 1- and 2-arachidonylglcerol eCB in muscle and liver were lower in the DHA diet group compared to controls. These findings demonstrate that DHA feeding in mice alters macronutrient metabolism and may restore ECS tone by lowering arachidonic acid derived eCB.
Clinically Evaluated COVID-19 Drugs with Therapeutic Potential for Biological Warfare Agents

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak resulted in hundreds of millions of coronavirus cases, as well as millions of deaths worldwide. Coronavirus Disease 2019 (COVID-19), the disease resulting from exposure to this pathogen, is characterized, among other features, by a pulmonary pathology, which can progress to “cytokine storm”, acute respiratory distress syndrome (ARDS), respiratory failure and death. Vaccines are the unsurpassed strategy for prevention and protection against the SARS-CoV-2 infection. However, there is still an extremely high number of severely ill people from at-risk populations. This may be attributed to waning immune response, variant-induced breakthrough infections, unvaccinated population, etc. It is therefore of high importance to utilize pharmacological-based treatments, despite the progression of the global vaccination campaign. Until the approval of Paxlovid, an efficient and highly selective anti-SARS-CoV-2 drug, and the broad-spectrum antiviral agent Lagevrio, many pharmacological-based countermeasures were, and still are, being evaluated in clinical trials. Some of these are host-directed therapies (HDTs), which modulate the endogenic response against the virus, and therefore may confer efficient protection against a wide array of pathogens. These could potentially include Biological Warfare Agents (BWAs), exposure to which may lead to mass casualties due to disease severity and a possible lack of efficient treatment. In this review, we assessed the recent literature on drugs under advanced clinical evaluation for COVID-19 with broad spectrum activity, including antiviral agents and HDTs, which may be relevant for future coping with BWAs, as well as with other agents, in particular respiratory infections.
Body Composition in Fussy-Eating Children, with and without Neurodevelopmental Disorders, and Their Parents, Following a Taste Education Intervention

Fussy eaters may have an increased risk of becoming overweight or obese as adolescents, with fussy eating and weight status also correlating with neurodevelopmental disorders (NDs) such as autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD). Further, maternal and children’s weight status relationships are well-established. In this study, we analyzed the body composition of parent–child dyads using bioelectrical impedance analysis (BIA). Fifty-one children aged 8–12 years, with an ND (n = 18) and without (n = 33), and their parents, participated in a 7-week food-based Taste Education intervention with 6-month follow-up. The paired t-test was used to compare differences in body composition based on children’s ND status. In logistic regression analysis, odds of children being in the overweight/obese or overfat/obese categories increased by a factor of 9.1 and 10.6, respectively, when having NDs, adjusting for parents’ BMI (body mass index) or fat percentage (FAT%). Children with NDs and their parents had significantly higher mean BMI-SDS (BMI standard deviation score) and FAT% at pre-intervention than children without NDs and their parents. Mean BMI-SDS and FAT% lowered significantly between time points for children with NDs and their parents but not for children without NDs or their parents. The findings underline the need for additional exploration into the relationships between children’s and parents’ body composition based on children’s ND status.
N-acetylcysteine improves autism-like behavior by recovering autophagic deficiency and decreasing Notch-1/Hes-1 pathway activity

N-acetylcysteine (NAC) has been reported to improve social interaction behavior, irritability, self-injury, and anxiety-like behavior in autism. However, the molecular mechanism underlying the therapeutic roles of NAC in autism remains unknown. This study mainly aimed to investigate the therapeutic effect of NAC on valproic acid (VPA)-induced autism model and the underlying mechanisms. Our results showed that NAC ameliorated the deficits in sociability and the anxiety- and repetitive-like behaviors displayed by VPA-exposed rats. In addition, VPA exposure induced autophagic deficiency and enhanced Notch-1/Hes-1 pathway activity based on lowered Beclin-1 and LC3B levels, while increased expression of p62, Notch-1, and Hes-1 expression at the protein level. However, NAC recovered VPA-induced autophagic deficiency and reduced Notch-1/Hes-1 pathway activity in a VPA-exposed autism rat model and SH-SY5Y neural cells. The present results demonstrated that NAC improves autism-like behavioral abnormalities by inactivating Notch-1/Hes-1 signaling pathway and recovering autophagic deficiency. Taken together, this study helps to elucidate a novel molecular mechanism that underlies the therapeutic actions of NAC in autism and suggests its potential to ameliorate behavioral abnormalities in neurodevelopmental disorders.
Erigeron annuus Extract Alleviates Insulin Resistance via Regulating the Expression of Mitochondrial Damage and Endoplasmic Reticulum Stress-Related Genes

Diabetes is a prevalent and debilitating metabolic disorder affecting a large population worldwide. The condition is characterized by insulin resistance and impaired function of pancreatic β-cells, leading to elevated blood glucose levels. In this study, the antidiabetic effects of Erigeron annuus extract (EAE) on zebrafish with damaged pancreatic islets caused by insulin resistance were investigated. The study utilized the zebrafish model to monitor live pancreatic islets. RNA sequencing was also conducted to determine the mechanism by which EAE exerts its antidiabetic effect. The results showed that EAE was effective in recovering reduced islets in excess insulin-induced zebrafish. The effective concentration at 50% (EC50) of EAE was determined to be 0.54 μg/mL, while the lethal concentration at 50% (LC50) was calculated as 202.5 μg/mL. RNA sequencing indicated that the mode of action of EAE is related to its ability to induce mitochondrial damage and suppress endoplasmic reticulum stress. The findings of this study demonstrate the efficacy and therapeutic potential of EAE in treating insulin resistance in zebrafish. The results suggest that EAE may offer a promising approach for the management of diabetes by reducing mitochondrial damage and suppressing endoplasmic reticulum stress. Further research is required to establish the clinical application of EAE in diabetic patients.
Effects of the Rashba and the Dresselhaus Spin-orbit Interactions on the Quantum Transport and Spin Filtering in a Three-terminal Quantum Ring

The spin resolved conductance in a quantum ring with one input and two output leads in the presence of the Rashba spin-orbit interaction (RSOI) and the Dresselhaus spin-orbit interaction (DSOI) has been studied. The conditions needed for perfect spin polarization including the value of the Rashba and Dresselhaus coupling strength and the values of the electron energy are investigated coupled strongly with the leads. Our calculations are performed using the non-equilibrium Green’s function method and Griffith boundary condition in the framework of the tight binding model. It is shown that the spin-polarized transport and polarizability can be controlled by the RSOI and/or DSOI in the effects of applied magnetic field treading the ring, but also on the bias applied between the input and output leads. Results of this paper can be used in designing perfect spin inverters. The effects of relative positions of the drain electrodes on the perfect spin polarization are also investigated.
A scoping review of current and emerging techniques for evaluation of peripheral nerve health, degeneration and regeneration: part 2, non-invasive imaging

Peripheral neuroregenerative research and therapeutic options are expanding exponentially. With this expansion comes an increasing need to reliably evaluate and quantify nerve health. Valid and responsive measures of the nerve status are essential for both clinical and research purposes for diagnosis, longitudinal follow-up, and monitoring the impact of any intervention. Furthermore, novel biomarkers can elucidate regenerative mechanisms and open new avenues for research. Without such measures, clinical decision-making is impaired, and research becomes more costly, time-consuming, and sometimes infeasible. Part 1 of this two-part scoping review focused on neurophysiology. In part 2, we identify and critically examine many current and emerging non-invasive imaging techniques that have the potential to evaluate peripheral nerve health, particularly from the perspective of regenerative therapies and research.
On anisotropic subgrid modeling

A modification of Smagorinsky's subgrid model is proposed to account for the effects of anisotropic filtering. No new empirical parameters are introduced by the modification. Numerical experiments for a low Reynolds number turbulent channel flow have been carried out. The results are in good agreement with results from direct numerical simulations. The effects of spatial resolution on the results of large eddy simulations are considered in some detail.
Nuclear Small Dystrophin Isoforms during Muscle Differentiation

Mutations in the DMD gene can cause Duchenne or Becker muscular dystrophy (DMD/BMD) by affecting the giant isoform of dystrophin, a protein encoded by the DMD gene. The role of small dystrophin isoforms is not well investigated yet, and they may play a role in muscle development and molecular pathology. Here, we investigated the nuclear localization of short carboxy-terminal dystrophin isoforms during the in vitro differentiation of human, porcine, and murine myoblast cultures. We could not only confirm the presence of Dp71 in the nucleoplasm and at the nuclear envelope, but we could also identify the Dp40 isoform in muscle nuclei. The localization of both isoforms over the first six days of differentiation was similar between human and porcine myoblasts, but murine myoblasts behaved differently. This highlights the importance of the porcine model in investigating DMD. We could also detect a wave-like pattern of nuclear presence of both Dp71 and Dp40, indicating a direct or indirect involvement in gene expression control during muscle differentiation.
Exploring the Potential of Fique Fiber as a Natural Composite Material: A Comprehensive Characterization Study

Many studies available in the literature focus mainly on the mechanical characterization of fiber, leaving out other physicochemical and thermogravimetric analyses that allow for establishing its potential as an engineering material. This study characterizes fique fiber for its potential use as an engineering material. The fiber’s chemical composition and physical, thermal, mechanical, and textile properties were analyzed. The fiber has a high holocellulose content and low lignin and pectin content, indicating its potential as a natural composite material for various applications. Infrared spectrum analysis revealed characteristic bands associated with multiple functional groups. The fiber had monofilaments with diameters around 10 μm and 200 μm, as determined by AFM and SEM images, respectively. Mechanical testing showed the fiber could resist a maximum stress of 355.07 MPa, with an average maximum strain at which breakage occurs of 8.7%. The textile characterization revealed a linear density range of 16.34 to 38.83 tex, with an average value of 25.54 tex and a regain of 13.67%. Thermal analysis showed that the fiber’s weight decreased by around 5% due to moisture removal in the range of 40 °C to 100 °C, followed by weight loss due to thermal degradation of hemicellulose and glycosidic linkages of cellulose ranging from 250 to 320 °C. These characteristics suggest that fique fiber can be used in industries such as packaging, construction, composites, and automotive, among others.
Muscle Traits, Sarcopenia, and Sarcopenic Obesity: A Vitamin D Mendelian Randomization Study

(1) Background: Observational studies associate vitamin D deficiency with muscle disorders, while some clinical trial data support a minor association between the vitamin and skeletal muscle performance in healthy subjects. Vitamin D receptor knockout mice studies confirm the relationship between vitamin D and skeletal muscle; however, causal inference in humans is challenging due to the ethical implications of including vitamin D-deficient participants in randomized trials. This study uses genetic methods to safely explore causal underpinnings for the relationship between 25(OH)D concentrations and skeletal muscle-related traits, including grip strength and combined arm skeletal muscle mass, and extends this analysis to suspected pathophysiology in the form of probable sarcopenia and sarcopenic obesity. (2) Methods: We conducted Mendelian randomization (MR) analyses in up to 307,281 participants from the UK Biobank of whom 25,414 had probable sarcopenia and 16,520 had sarcopenic obesity. In total, 35 variants were used to instrument 25(OH)D and MR analyses conducted using multiple approaches. (3) Results: Genetic analyses provided support for a relationship between genetically predicted higher 25(OH)D and skeletal muscle traits, with linear MR analyses for grip strength showing 0.11 kg (95% CI 0.04, 0.19) greater contractile force per 10 unit higher 25(OH)D, while there was a modest association with skeletal muscle mass (0.01 kg (95% CI 0.003, 0.02) greater muscle mass). For probable sarcopenia risk, there was suggestive evidence for lower odds by higher 25(OH)D (OR 0.96 (95% CI 0.92, 1.00)); however, this did not reflect an association with sarcopenic obesity (OR 0.97 (95% CI 0.93, 1.02)), but was seen in probable sarcopenia cases who were not obese (OR 0.92 (95% CI 0.86, 0.98)). Results were similar across multiple MR approaches. (4) Conclusions: Our study supports a causal relationship between 25(OH)D and skeletal muscle health. While evidence for benefit did not extend to lower risk of sarcopenic obesity, effective vitamin D-deficiency prevention strategies may help reduce age-related muscle weakness.
Harmonic Vibrational Frequency Simulation of Pharmaceutical Molecules via a Novel Multi-Molecular Fragment Interception Method

By means of a computational method based on Density Functional Theory (DFT), using commercially available software, a novel method for simulating equilibrium geometry harmonic vibrational frequencies is proposed. Finasteride, Lamivudine, and Repaglinide were selected as model molecules to study the adaptability of the new method. Three molecular models, namely the single-molecular, central-molecular, and multi-molecular fragment models, were constructed and calculated by Generalized Gradient Approximations (GGAs) with the PBE functional via the Material Studio 8.0 program. Theoretical vibrational frequencies were assigned and compared to the corresponding experimental data. The results indicated that the traditional single-molecular calculation and scaled spectra with scale factor exhibited the worst similarity for all three pharmaceutical molecules among the three models. Furthermore, the central-molecular model with a configuration closer to the empirical structure resulted in a reduction of mean absolute error (MAE) and root mean squared error (RMSE) in all three pharmaceutics, including the hydrogen-bonded functional groups. However, the improvement in computational accuracy for different drug molecules using the central-molecular model for vibrational frequency calculation was unstable. Whereas, the new multi-molecular fragment interception method showed the best agreement with experimental results, exhibiting MAE and RMSE values of 8.21 cm−1 and 18.35 cm−1 for Finasteride, 15.95 cm−1 and 26.46 cm−1 for Lamivudine, and 12.10 cm−1 and 25.82 cm−1 for Repaglinide. Additionally, this work provides comprehensive vibrational frequency calculations and assignments for Finasteride, Lamivudine, and Repaglinide, which have never been thoroughly investigated in previous research.
Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson–Boltzmann Theories

The current SARS-CoV-2 pandemic highlights our fragility when we are exposed to emergent viruses either directly or through zoonotic diseases. Fortunately, our knowledge of the biology of those viruses is improving. In particular, we have more and more structural information on virions, i.e., the infective form of a virus that includes its genomic material and surrounding protective capsid, and on their gene products. It is important to have methods that enable the analyses of structural information on such large macromolecular systems. We review some of those methods in this paper. We focus on understanding the geometry of virions and viral structural proteins, their dynamics, and their energetics, with the ambition that this understanding can help design antiviral agents. We discuss those methods in light of the specificities of those structures, mainly that they are huge. We focus on three of our own methods based on the alpha shape theory for computing geometry, normal mode analyses to study dynamics, and modified Poisson–Boltzmann theories to study the organization of ions and co-solvent and solvent molecules around biomacromolecules. The corresponding software has computing times that are compatible with the use of regular desktop computers. We show examples of their applications on some outer shells and structural proteins of the West Nile Virus.