Miracle-dz/UniFAR-FTUs huggingface dataset:
Scaling of Long-Term Seismicity in Zagros, Iran

The long-term Precursory Scale Increase (Y) phenomenon is used to relate minor seismicity to major shallow earthquakes in Zagros. This phenomenon involves an increase in the magnitude and rate of occurrence of minor earthquakes in an area near to the location of a major event. By the modeling of long-term seismogenesis as a three-stage faulting process, the Precursory Scale Increase (Y) phenomenon can be inferred. Scaling characterizes the parameters of space, time and magnitude that relate the precursory seismicity to the main shock and aftershocks. Seismogenesis starts with the formation of a major crack, culminates in the corresponding major fracture and earthquake, and ends with healing. Showing high seismicity in southwest of Iran, Zagros mountain accommodate major part of convergence between Arabia and Eurasia. From 1970 to 2009, 29 earthquakes in this region demonstrated a sudden increase in the scale of seismicity, which can be inferred as a long-term precursor. Range of magnitudes of these earthquakes was from5.6 to 6.7. Precursory time (TP) interval between onset of the scale increase and occurrence of the earthquake, and the precursory space (AP) that involved space-time is optimized respectively to scale increase. By scaling relations, predictive regressions are found between the magnitude level of the precursory seismicity (MP) versus TP, AP and the main earthquake magnitude separately. As these relations show high goodness of fit for Zagros, the method could be used in long-range forecasting of the place, time and magnitude of major earthquakes in Zagros region.
Oil-in-Water Pickering Emulsions Stabilized with Nanostructured Biopolymers: A Venue for Templating Bacterial Cellulose

Pickering emulsions (PEs) differ from conventional emulsions in the use of solid colloidal particles as stabilizing agents instead of traditional amphiphilic molecules. Nanostructured biopolymers (NBs) emerge as a promising alternative for PE stabilization owing to their remarkable biocompatibility, abundant availability, and low cost. To explore this potential, a study is herein presented, in which cellulose nanocrystals (CNCs), both type I and type II allomorphs, and chitin nanocrystals (ChNCs) were used for stabilizing oil-in-water PEs prepared by the use of ultrasound. Sunflower oil was selected as the oil phase as it offers the advantages of being edible, renewable, and inexpensive. By utilizing ζ-potential, static light diffraction, and visual observations, we determined the optimal oil/water ratio for each type of NB to obtain stable emulsions after 14 days. The optimized PEs were used to form bacterial nanocellulose composites through emulsion templating. To our knowledge, this study represents a pioneering work in exploiting oil-in-water PEs for this approach. Additionally, it entails the first utilization of nonmercerized type II CNCs as stabilizers for PEs, while also establishing a direct comparison among the most relevant NBs. The resulting composites exhibited a unique morphology, composed of larger pores compared to standard bacterial nanocellulose aerogels. These findings highlight the notable potential of NBs as stabilizers for PEs and their ability to generate green nanocomposites with tailored properties.
A General Hierarchical Control System to Model ACC Systems: An Empirical Study

Urged by a close future perspective of a traffic flow made of a mix of human-driven vehicles and automated vehicles (AVs), research has recently focused on studying the traffic flow characteristics of Adaptive Cruise Controls (ACCs), the most typical AV. However, in most works, the ACC system is studied under a simplifying and unrealistic assumption, or the ACC system modeled is inaccurate. This paper proposes a general hierarchical control system to model ACC systems with several assumptions based on the deficiencies above. Moreover, a field experiment was conducted, and the corresponding experimental data was used to verify the proposed hierarchical control system and assumptions. In addition, string stability is explored along with sensitivity analyses of control parameters based on an example under the constant time gap policy. The results show that different upper-level controller parameters have different delays, where the delay of the speed is negligible; the introduction of actuator delay and lag in the lower-level controller can significantly improve the model goodness of fit. Furthermore, optimizing the delay and lag in the lower-level controller can significantly enhance the string stability of ACCs than optimizing the control parameters.
The Numerical Analysis of Force and Comparison of Pulse Magnet and Electromagnetic Forming Coil

As an important energy conversion component in electromagnetic-forming technology, the coil is subjected to great internal stress and is easy to break. The geometric structure and winding process of the forming coil draw on the research results of pulsed magnets. However, the two use conditions are different. It is very important to clarify the force difference between the two for the design of the forming coil. In this paper, the numerical model of an aluminum alloy (AA1060-O) is established, and the difference in force between the pulse magnet and forming coil with the same size in time and space under different working conditions is analyzed. A two-dimensional fully coupled finite element model consisting of circuit, magnetic field, and solid mechanics is established and used to determine the key parts of the coil force. It is found that the von Mises stress of the forming coil is greater than that of the pulsed magnet under the same circuit parameters and geometric structure. In the electromagnetic forming of the tube, the glass fiber is subjected to a large stress. In addition, the stress of glass fiber under the condition of tube necking is about 2 times that of pulsed magnet. When the voltage is increased, the failure of the middle part of the glass fiber causes the coil to break. In the electromagnetic forming of the sheet, the coil skeleton is subjected to large stress, and its upper end failure causes the coil to break. Therefore, new design ideas for forming coils under different working conditions are proposed.
Optimized Tensor Decomposition and Principal Component Analysis Outperforming State-of-the-Art Methods When Analyzing Histone Modification Chromatin Immunoprecipitation Profiles

It is difficult to identify histone modification from datasets that contain high-throughput sequencing data. Although multiple methods have been developed to identify histone modification, most of these methods are not specific to histone modification but are general methods that aim to identify protein binding to the genome. In this study, tensor decomposition (TD) and principal component analysis (PCA)-based unsupervised feature extraction with optimized standard deviation were successfully applied to gene expression and DNA methylation. The proposed method was used to identify histone modification. Histone modification along the genome is binned within the region of length L. Considering principal components (PCs) or singular value vectors (SVVs) that PCA or TD attributes to samples, we can select PCs or SVVs attributed to regions. The selected PCs and SVVs further attribute p-values to regions, and adjusted p-values are used to select regions. The proposed method identified various histone modifications successfully and outperformed various state-of-the-art methods. This method is expected to serve as a de facto standard method to identify histone modification. For reproducibility and to ensure the systematic analysis of our study is applicable to datasets from different gene expression experiments, we have made our tools publicly available for download from gitHub.
Mitigation of greenhouse gas emissions in the French winter oilseed rape in order to produce sustainable biodiesel

The European Union decided to promote biofuels in order to decrease the emissions of greenhouse gas (GHG) and the importation of non-renewable energy (Directive 2003/30/EC). The biofuels used in Europe must fulfil sustainability criteria including a minimum saving in GHG compared to the non-renewable fuel (Directive 2009/28/EC). The minimum saving value is 35% and will be increased to 50% in 2017. Hence, the GHG emissions of crops producing the raw materials for biofuels are key issues.
Heterogeneity in macrophages along the cochlear spiral in mice: insights from SEM and functional analyses

The susceptibility of sensory cells to pathological conditions differs between the apical and basal regions of the cochlea, and the cochlear immune system may contribute to this location-dependent variability. Our previous study found morphological differences in basilar membrane macrophages between the apical and basal regions of the cochlea. However, the details of this site-dependent difference and its underlying structural and biological basis are not fully understood. In this study, we utilized scanning electron microscopy to examine the ultrastructure of macrophages and their surrounding supporting structures. Additionally, we examined the phagocytic activities of macrophages and the expression of immune molecules in both apical and basal regions of the cochlea. We employed two mouse strains (C57BL/6J and B6.129P-Cx3cr1tm1Litt/J) and evaluated three experimental conditions: young normal (1–4 months), aging (11–19 months), and noise-induced damage (120 dB SPL for 1 h). Using scanning electron microscopy, we revealed location-specific differences in basilar membrane macrophage morphology and surface texture, architecture in mesothelial cell layers, and spatial correlation between macrophages and mesothelial cells in both young and older mice. Observations of macrophage phagocytic activities demonstrated that basal macrophages exhibited greater phagocytic activities in aging and noise-damaged ears. Furthermore, we identified differences in the expression of immune molecules between the apical and basal cochlear tissues of young mice. Finally, our study demonstrated that as the cochlea ages, macrophages in the apical and basal regions undergo a transformation in their morphologies, with apical macrophages acquiring certain basal macrophage features and vice versa. Overall, our findings demonstrate apical and basal differences in macrophage phenotypes and functionality, which are related to distinct immune and structural differences in the macrophage surrounding tissues.
The causal relationship between multiple autoimmune diseases and nasal polyps

Background Although previous sporadic studies have reported the associations between a few autoimmune diseases and nasal polyps, these studies have limitations such as conflicting results, small sample sizes, and low levels of evidence. Methods Several autoimmune diseases were selected as exposures while the nasal polyps were selected as outcomes. Bidirectional univariable Mendelian randomization and multivariable Mendelian randomization analyses were performed after rigorous screening of instrumental variables. Then mediation analyses were conducted to further investigate the underlying mechanisms. Results For the first time, we investigated the causal relationships between nine autoimmune diseases and nasal polyps in different genders and found: (1) there was a causal association between adult-onset Still's disease and nasal polyps; (2) sarcoidosis, ulcerative colitis, type 1 diabetes, and Crohn’s disease had no significant associations with nasal polyps; (3) celiac disease showed a suggestive positive association with female nasal polyps, whereas juvenile arthritis and multiple sclerosis showed suggestive positive associations with male nasal polyps. By contrast, arthropathic psoriasis showed a suggestive negative association with nasal polyps. In addition to these nine diseases, previous controversial issues were further investigated: (1) there was a causal relationship between rheumatoid arthritis and nasal polyps, which was partially mediated by “BAFF-R for IgD+ B cells”; (2) ankylosing spondylitis showed suggestive positive associations with the female but not the male nasal polyps. Besides, we validated that there was no causal effect of autoimmune hyperthyroidism on nasal polyps. Conclusion Specific conclusions regarding the causal effects of multiple autoimmune diseases on nasal polyps are the same as above. By comparing results between different genders, we have initially observed the sex bimodality in the causal effects between autoimmune diseases and nasal polyps, with those on male nasal polyps being stronger than those on female nasal polyps. Our study lays a solid foundation for further research in the future, not only helping identify individuals susceptible to nasal polyps early but also improving our understanding of the immunopathogenesis of these heterogeneous diseases.
ISOENZYMATIC VARIATION OF MAIZE LANDRACES FROM THE REGION LLANOS DE SERDÁN, PUEBLA

In order to explore the isoenzymatic variation, the degree of genetic differentiation and phylogenetic relationships of native populations of maize (Zea mays L. spp. mays) of the Llanos de Serdan region, Puebla, we studied 51 collections from 10 municipalities in Libres' Rural Development District and six controls, representatives of Conico, Conico Norteno, Palomero Toluqueno and Chalqueno races. Ten enzyme systems encoding for 18 loci were examined, where 52 alleles were detected. Based on allele frequencies, the genetic diversity parameters were estimated, finding that the entire native population presented 98% of the total alleles, with nine exclusives, with an average of 2.83 alleles per locus, 88.9% of polymorphic loci and expected heterozygosity 0.27. Moderate genetic differentiation (0.085) was found, indicating that only 8.5% of the variation was between groups and 91.5% within the groups. The native populations had a higher genetic similarity with Chalqueno race, although they are diverging from it, possibly because of the selection practiced by farmers in the area.
Methane Production by a Packed-Bed Anaerobic Digester Fed Dairy Barn Flush Water

Packed-bed digesters are an alternative to covered lagoon digesters for methane production and anaerobic treatment of dilute wastewaters such as dairy barn flush water. The physical media of packed-beds retain biofilms, often allowing increased treatment rates. Previous studies have evaluated several types of media for digestion of dilute wastewaters, but cost and media fouling have setback commercial development. A major operational cost has been effluent recirculation pumping. In the present effort, a novel approach to anaerobic digestion of flush dairy water was developed at pilot-scale: broken walnut shells were used as a low-cost packed-bed medium and effluent recirculation was replaced by reciprocation mixing to decrease pumping costs and the risk of media clogging. Three packed-bed digesters containing walnut shells as media were constructed at the on-campus dairy and studied for about six months. Over that time, several organic loading rates (OLRs), measured as both chemical oxygen demand (COD) and volatile solids (VS) were applied to the new packed-bed digesters to allow modeling of methane production. The influence of temperature on methane production was also investigated. Additionally, the study measured solids accumulation in the walnut shell packed-bed as well as the effectiveness and durability of walnut shells as packing media. Finally, a simple economic analysis was developed from the methane model to predict the financial feasibility of packed-bed digesters at flush water dairies under similar OLR conditions. v Three methane production models were developed from organic loading: saturation-type (following the form of the Monod equation), power and linear. The models were evaluated in terms of regression analysis and the linearity of experimental to predicted methane production. The best model was then chosen to develop the economic predictions. Economic predictions for packed-bed digesters were calculated as internal rate of return (IRR) using the methane models along with additional input variables. Comparisons of IRRs were made using electric retail rates of $0.10 to $0.20 per kilowatt-hour and capital cost subsidies from zero to 50%. Sludge accumulation in the packed-bed was measured via change in porosity, and walnut shell durability was measured as the change in mass of representative walnut shells over the course of the study. The linear-type model of methane production from volatile solids OLR best represented this data set. Digester temperature was not found to influence methane production in this study, likely due to the small daily average ambient temperature range experienced (14°C to 24°C) and the greater influence of organic …
Modifications to the Theory of Intraglacial Waterways for the Case of Subglacial Ones

Abstract It is argued that in temperate mountain glaciers, waterways are subglacial. It is shown that the theory of Spring and Hutter (1981) for intraglacial flooded conduits leads to an equation for the grade line which differs from Röthlisberger’s (1972) only by negligible terms, and a slight modification of the exponent of the discharge. For a subglacial flooded waterway two important processes should instead be introduced: the enhancement of plastic deformation on the up-stream side of bumps, and the heat afforded by ground water (which in winter accounts for most of the discharge). The theory modified in this way explains why Röthlisberger had to adopt an unrealistic value for the rheological parameter of ice. It leads to the conclusion that in areas which are not overdeepened, most of the year subglacial waterways should remain not flooded and at atmospheric pressure. The case of overdeepening is examined. Finally the implications of this new model for glacier sliding theory are demonstrated.
Role of the Lactide:Glycolide Ratio in PLGA Nanoparticle Stability and Release under Lysosomal Conditions for Enzyme Replacement Therapy of Lysosomal Storage Disorders

Prior studies demonstrated that encapsulation in poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) enhanced the delivery of enzymes used for replacement therapy (ERT) of lysosomal storage disorders (LSDs). This study examined how the copolymer lactide:glycolide ratio impacts encapsulation, physicochemical characteristics, stability, and release under lysosomal conditions. Hyaluronidase, deficient in mucopolysaccharidosis IX, was encapsulated in NPs synthesized using 50:50, 60:40, or 75:25 lactide:glycolide copolymers. All NPs had diameters compatible with cellular transport (≤168 nm) and polydispersity indexes (≤0.16) and ζ-potentials (≤−35 mV) compatible with colloidal stability. Yet, their encapsulation efficiency varied, with 75:25 NPs and 60:40 NPs having the lowest and highest EE, respectively (15% vs. 28%). Under lysosomal conditions, the 50:50 copolymer degraded fastest (41% in 1 week), as expected, and the presence of a targeting antibody coat did not alter this result. Additionally, 60:40 NPs destabilized fastest (<1 week) because of their smaller diameter, and 75:25 NPs did not destabilize in 4 weeks. All formulations presented burst release under lysosomal conditions (56–78% of the original load within 30 min), with 50:50 and 60:40 NPs releasing an additional small fraction after week 1. This provided 4 weeks of sustained catalytic activity, sufficient to fully degrade a substrate. Altogether, the 60:40 NP formulation is preferred given its higher EE, and 50:50 NPs represent a valid alternative, while the highest stability of 75:25 NPs may impair lysosomes. These results can guide future studies aiming to translate PLGA NP-based ERT for this and other LSDs.
Identification of potential pathogenic targets and survival strategies of Vibrio vulnificus through population genomics

Vibrio vulnificus, a foodborne pathogen, has a high mortality rate. Despite its relevance to public health, the identification of virulence genes associated with the pathogenicity of currently known clinical isolates of V. vulnificus is incomplete and its synergistic pathogenesis remains unclear. Here, we integrate whole genome sequencing (WGS), genome-wide association studies (GWAS), and genome-wide epistasis studies (GWES), along with phenotype characterization to investigate the pathogenesis and survival strategies of V. vulnificus. GWAS and GWES identified a total of six genes (purH, gmr, yiaV, dsbD, ramA, and wbpA) associated with the pathogenicity of clinical isolates related to nucleotide/amino acid transport and metabolism, cell membrane biogenesis, signal transduction mechanisms, and protein turnover. Of these, five were newly discovered potential specific virulence genes of V. vulnificus in this study. Furthermore, GWES combined with phenotype experiments indicated that V. vulnificus isolates were clustered into two ecological groups (EGs) that shared distinct biotic and abiotic factors, and ecological strategies. Our study reveals pathogenic mechanisms and their evolution in V. vulnificus to provide a solid foundation for designing new vaccines and therapeutic targets.
Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis

Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait’s marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative Escherichia coli, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs’ prevalence in E. coli isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and intl1 (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (blaCMY-150, blaCMY-42, blaCTX-M-15, blaDHA-1, blaMIR-1, blaOKP-B-15, blaOXA-1, blaOXA-48, blaTEM-1B, blaTEM-35), trimethoprim (dfrA14, dfrA15, dfrA16, dfrA1, dfrA5, dfrA7), fluroquinolone (oqxA, oqxB, qnrB38, qnrB4, qnrS1), aminoglycoside (aadA2, ant(3’’)-Ia, aph(3’’)-Ib, aph(3’)-Ia, aph(6)-Id), fosfomycin (fosA7, fosA_6, fosA, fosB1), sulfonamide (sul1, sul2, sul3), tetracycline (tet-A, tet-B), and macrolide (mph-A). The MFS-type drug efflux gene mdf-A is also quite common in E. coli isolates (80%). The plasmid ColRNAI was also found to be prevalent in E. coli. The integron gene intI1 and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total E. coli isolates. A positive and significant (p < 0.001) correlation was observed between phenotypic AMR-intl1 (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.