Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive Analysis of the lncRNA–miRNA–mRNA Regulatory Network for Intramuscular Fat in Pigs

Intramuscular fat (IMF) is an essential trait closely related to meat quality. The IMF trait is a complex quantitative trait that is regulated by multiple genes. In order to better understand the process of IMF and explore the key factors affecting IMF deposition, we identified differentially expressed mRNA, miRNA, and lncRNA in the longissimus dorsi muscle (LD) between Songliao Black (SL) pigs and Landrace pigs. We obtained 606 differentially expressed genes (DEGs), 55 differentially expressed miRNAs (DEMs), and 30 differentially expressed lncRNAs (DELs) between the SL pig and Landrace pig. Enrichment results from GO and KEGG indicate that DEGs are involved in fatty acid metabolism and some pathways related to glycogen synthesis. We constructed an lncRNA–miRNA–mRNA interaction network with 18 DELs, 11 DEMs, and 42 DEGs. Finally, the research suggests that ARID5B, CPT1B, ACSL1, LPIN1, HSP90AA1, IRS1, IRS2, PIK3CA, PIK3CB, and PLIN2 may be the key genes affecting IMF deposition. The LncRNAs MSTRG.19948. 1, MSTRG.13120. 1, MSTRG.20210. 1, and MSTRG.10023. 1, and the miRNAs ssc-miRNA-429 and ssc-miRNA-7-1, may play a regulatory role in IMF deposition through their respective target genes. Our research provides a reference for further understanding the regulatory mechanism of IMF.
Whole genome sequencing and functional analysis of porcine-borne Bacillus coagulans LYBC06

Abstract Bacillus coagulans LYBC06 strain with lactate-producing capacity was isolated from mucosal tissue of the digestive tract of a fattening pig. The resequencing of the LYBC06 strain revealed that the overall genome was less variable, with a genome-wide heterozygous ratio of 0.042 %, total SNP locus variants 0.4273% of the entire genome, total InDel mutations 0.0182%, total increased and decreased CNV copies 0.0031% and total SV annotated variants 0.0083% of the entire genome. The mutated genes were mainly involved in the growth of the strain, regulation of energy metabolism, and production of proteases and lactate. The whole genome of LYBC06 strain was sequenced with the length of 3385106 bp, GC content of 46.86% and 4092 coding genes (85.96% of coding). Functional annotation of the proteins encoding genes showed that the growth process of LYBC06 strain involved several metabolic pathway transformation processes of various substances, and many encoding genes were involved in the resistance to macrolides, polypeptides and tetracyclines. The basic characteristics of the genome of LYBC06 strain were relatively similar to those of other Bacillus coagulans, and the collinearity between several Bacillus coagulans strains was relatively good. Bacterial growth, gene expression of lactate dehydrogenase and lactate production in LYBC06 strain were largely synchronized, and the maximum amount of lactate could be produced up to 92 g/L at 16 h culture during the logarithmic growth phase, in which the LdhL1 gene played an important role in the production of lactate in LYBC06 strain.
Liver Regeneration and Immunity: A Tale to Tell

The physiological importance of the liver is demonstrated by its unique and essential ability to regenerate following extensive injuries affecting its function. By regenerating, the liver reacts to hepatic damage and thus enables homeostasis to be restored. The aim of this review is to add new findings that integrate the regenerative pathway to the current knowledge. An optimal regeneration is achieved through the integration of two main pathways: IL-6/JAK/STAT3, which promotes hepatocyte proliferation, and PI3K/PDK1/Akt, which in turn enhances cell growth. Proliferation and cell growth are events that must be balanced during the three phases of the regenerative process: initiation, proliferation and termination. Achieving the correct liver/body weight ratio is ensured by several pathways as extracellular matrix signalling, apoptosis through caspase-3 activation, and molecules including transforming growth factor-beta, and cyclic adenosine monophosphate. The actors involved in the regenerative process are numerous and many of them are also pivotal players in both the immune and non-immune inflammatory process, that is observed in the early stages of hepatic regeneration. Balance of Th17/Treg is important in liver inflammatory process outcomes. Knowledge of liver regeneration will allow a more detailed characterisation of the molecular mechanisms that are crucial in the interplay between proliferation and inflammation.
Carbon Dot Emission Enhancement in Covalent Complexes with Plasmonic Metal Nanoparticles

Carbon dots can be used for the fabrication of colloidal multi-purpose complexes for sensing and bio-visualization due to their easy and scalable synthesis, control of their spectral responses over a wide spectral range, and possibility of surface functionalization to meet the application task. Here, we developed a chemical protocol of colloidal complex formation via covalent bonding between carbon dots and plasmonic metal nanoparticles in order to influence and improve their fluorescence. We demonstrate how interactions between carbon dots and metal nanoparticles in the formed complexes, and thus their optical responses, depend on the type of bonds between particles, the architecture of the complexes, and the degree of overlapping of absorption and emission of carbon dots with the plasmon resonance of metals. For the most optimized architecture, emission enhancement reaching up to 5.4- and 4.9-fold for complexes with silver and gold nanoparticles has been achieved, respectively. Our study expands the toolkit of functional materials based on carbon dots for applications in photonics and biomedicine to photonics.
Parametrically pumped ultrahigh Q electromechanical resonator

The spectral purity of an electromechanical resonance (quality factor Q) can be enhanced by more than one order of magnitude to ∼2.5×106 by parametrically exciting the fundamental mode via double frequency modulations to the spring constant mediated by the piezoelectric effect. We theoretically demonstrate that this Q enhancement is an intrinsic property of the parametric resonator by solving the equation of motion for this system. The Q enhancement demonstrated here results in smaller perturbations in the resonance (∼0.05Hz) becoming visible which enables the charge sensitivity of the electromechanical oscillator to improve by a factor equal to the Q enhancement.
Evaluation of prototype risk prediction tools for clinicians and people living with type 2 diabetes in North West London using the think aloud method

The prevalence of type 2 diabetes in North West London (NWL) is relatively high compared to other parts of the United Kingdom with outcomes suboptimal. This presents a need for more effective strategies to identify people living with type 2 diabetes who need additional support. An emerging subset of web-based interventions for diabetes self-management and population management has used artificial intelligence and machine learning models to stratify the risk of complications from diabetes and identify patients in need of immediate support. In this study, two prototype risk prediction tools on the MyWay Diabetes and MyWay Clinical platforms were evaluated with six clinicians and six people living with type 2 diabetes in NWL using the think aloud method. The results of the sessions with people living with type 2 diabetes showed that the concept of the tool was intuitive, however, more instruction on how to correctly use the risk prediction tool would be valuable. The feedback from the sessions with clinicians was that the data presented in the tool aligned with the key diabetes targets in NWL, and that this would be useful for identifying and inviting patients to the practice who are overdue for tests and at risk of complications. The findings of the evaluation have been used to support the development of the prototype risk predictions tools. This study demonstrates the value of conducting usability testing on web-based interventions designed to support the targeted management of type 2 diabetes in local communities.
Stochastic image reconstruction in bioluminescence tomography with the equation of radiative transfer

The underlying mathematical model for bioluminescence tomography (BLT) is an ill-posed inverse source problem, which can be cast into an optimization problem of a χ2-error function. The error function quantifies the discrepancy between the measured and predicted partial current of bioluminescent light at the tissue boundary. In this work, the predicted partial current has been calculated prior to image reconstruction by solving the equation of radiative transfer (ERT) for a set of source basis functions of the entire tissue domain. A global optimization technique based on stochastic sampling principles probes the global parameter space of bioluminescent source distributions composed of source basis functions. The stochastic approach avoids a premature convergence, which can be caused, e.g., by a narrow or a shallow surface landscape of the χ2-error function. Initial reconstruction results are compared to gradient-based image reconstructions.
Adaptive phase change metamaterials for infrared aperture control

This paper discusses the use of chalcogenide phase change materials to create tunable metamaterials as potential candidates for application to adaptive coded aperture control in the infrared. Phase change materials exhibit large and reversible changes in optical properties (Δn, Δk) when switched between the amorphous and crystalline phases. Thermally-induced phase transitions from the insulating amorphous to the conductive crystalline state can be controlled through external means, facilitating the design of reconfigurable metamaterial devices that operate with ultrafast response times. In this work, robust global stochastic optimization algorithms were combined with full-wave electromagnetic simulation tools to design periodic subwavelength chalcogenide nanostructured arrays to meet the specified device performance goals in each phase. The measured optical properties (n, k) of deposited chalcogenide thin films and nanofabrication constraints were incorporated into the optimization algorithm to guarantee that the designed nanostructures could be manufactured. By choosing the appropriate cost functions, adaptive metamaterials were designed to switch between transmissive and reflective, transmissive and absorptive, and reflective and absorptive states. These design demonstrations represent a significant step forward in the development of adaptive infrared metamaterials.
Imaging through the atmosphere: practical instrumentation-based theory and verification of aerosol modulation transfer function: reply to comment

New exact numerical calculations as well as exact calculations in J. Opt. Soc. Am. A10, 172 ( 1993) indicate that the approximations in the Comment in J. Opt. Soc. Am. A11, 1175 ( 1994) are based on faulty perceptions of basic scattering phenomena and on a misreading of our paper. The Comment does not sufficiently consider effects of instrumentation. Whereas our model refers to the aerosol modulation transfer function (MTF) in the image plane, the values of maximum angles for scattered (θS) and unscattered (θ0) light used in the Comment refer to the optics plane. The Comment does not consider the fact that dynamic range limits (θS) in the image, whereas limited spatial-frequency bandwidth broadens θ0 in the image, each by orders of magnitude. Therefore the Comment’s conclusion contradicts experimental results obtained by numerous researchers. The Comment’s conclusion that aerosol MTF is insignificant is based on that author’s own experiments, in which clear weather and haze atmospheric MTF (composed of turbulence and aerosol MTF’s) could not be measured, the reason being insufficient equipment resolution, rather than insignificant turbulence or aerosol MTF. Furthermore, the claim in our original paper that aerosol MTF is extremely significant has since been supported by many different types of experiments that included short and long exposures, thermal imaging, and image restoration based on atmospheric MTF, including a highly significant practical, uniquely shaped, aerosol MTF.
Wireless Powered Cooperative NOMA With Alamouti Coding and Selection Relaying

Nonorthogonal multiple access (NOMA) can facilitate simultaneous data transmissions towards multiple users by using the superposition coding and successive interference cancelation techniques, which can greatly improve the spectrum efficiency. Cooperative relaying and space-time coding can promisingly improve the communication robustness of poor-quality links by achieving the space-diversity gain. Energy harvesting (EH) can prolong the lifetime of energy-limited terminals and make them work continuously. In order to enhance the spectrum efficiency as well as the communication quality, we enable a cluster of EH relays to assist the data transmissions from a base station (BS) to two far-users by using the Alamouti coding based cooperative NOMA strategy. The relays are capable of harvesting wireless energy from a power beacon as well as BS by using time-switching or power-splitting method. According to the energy status and the data decoding status, one relay is selected in a distributed manner according to either Max-min, Max-sum, or Random criterion. We analyze the transmission success probability and the system throughput performance. Extensive simulations are performed to compare the performance of different EH-based space-time coded cooperative NOMA with various relay selection schemes as well as the counterpart orthogonal transmission schemes.
Nonlinear Rayleigh-Taylor instability in hydromagnetics

Nonlinear Rayleigh-Taylor instability of a heavy, infinitely conducting fluid, supported against gravity by a uniform magnetic field in the vacuum, is studied for three-dimensional disturbances using the method of multiple time-scales. The three-dimensional problem can be reduced to two dimensions as it is found that an instability present for a three-dimensional disturbance of a given wavelength, for a given equilibrium magnetic field, is also present for a two-dimensional disturbance of the same wavelength propagating along an equilibrium magnetic field of lower strength. The instability is studied for both standing and progressive waves. Although in the linear stability problem the instability growth rate for a progressive wave of a given wavelength is equal to that for a stationary wave of the same wavelength, in the nonlinear instability problem studied here these waves are found to have different growth rates. Our results are compared and contrasted with those for the two-dimensional instability problem studied earlier.
Quantitative risk assessment in epidemiological studies investigating threshold effects

In this paper a method for quantitative risk assessment in epidemiological studies investigating threshold effects is proposed. The simple logistic regression model is used to describe the association between a binary response variable and a continuous risk factor. By defining acceptable levels for the absolute risk and the risk gradient the corresponding benchmark values of the risk factor can be calculated by means of nonlinear functions of the logistic regression coefficients. Standard errors and confidence intervals of the benchmark values are derived by means of the multivariate delta method. The proposed approach is compared with the threshold model of Ulm (1991) for assessing threshold values in epidemiological studies.
Predictive Cruise Control Under Cloud Control System for Urban Bus Considering Queue Dissipation Time

The driving conditions of urban consecutive signalized intersections are one of the main research scenarios for vehicle speed trajectory optimization, and typical for bus driving, where frequent acceleration and deceleration before and after the intersection can intensify the energy consumption of the bus. Prior research has predictive cruise controlled under Intelligent Transportation System, which is not feasible to directly communicate with controllers’ units of Intelligent Connected Vehicles. Besides, the effect of queue dissipation is a topic that has received less attention in recent related work. Therefore, this paper proposes a vehicle-cloud hierarchical architecture based on Cloud Control System at first, under which a predictive cruise control for urban buses is deployed. Given the impact of intersection queue length and dissipation time on vehicle driving, a queue dissipation time estimation model based on shockwave theory is proposed to predict changes in intersection traffic state. The queue dissipation time equivalent to the extension of the red-light window is reflected in the constraints of the Receding Distance Horizon Dynamic Programming (RDHDP) algorithm for solving the optimal control problem. Eventually, comparison simulations, a segment of realistic trip between adjacent stops, are presented. The results show that the proposed method saves 44.94%–56.74% of energy consumption and at least 26.8s of waiting time compared to human drivers, and 22.72%–41.27% of energy consumption compared to vehicle with the Intelligent Vehicle Infrastructure Cooperative Systems.
An Experimental Anodized Titanium Surface for Transgingival Dental Implant Elements—Preliminary Report

The characteristics such as microtopography, physical and chemical properties influence the behavior of an implant in a soft tissue. Anodization—as a potent method of titanium alloy surface modification—of the transgingival abutment or healing screw, has achieved some improvement. One of the possible surface treatment method is low-pressure radiofrequency oxygen plasma treatment. The aim of the study was to evaluate the chemical properties and cytocompatibility of the experimental surface. Titanium discs made of grade-23 titanium alloy (Ti-6Al-4V) anodized (A sample) with different voltage parameters (28, 67, 78, and 98 V) were included in the study. Half of the samples regarded as the “S” group were additionally treated with low-pressure radiofrequency oxygen plasma treatment. The surfaces were characterized using scanning electron microscopy, X-ray spectroscopy and Raman spectroscopy, and electrochemically investigated via a corrosion test. Furthermore, two cell lines were used, including the CHO-compatible reference line and a primary human fibroblast line for the MTT assay; direct (contact) cytotoxicity of the materials was tested with the cells, and the growth of fibroblasts on the surfaces of the different materials was tested. The morphology of the “S”-treated samples did not differ from the morphology of only-anodized samples. However, the oxygen concentration on the surface in that group slightly increased by about 1% as a result of post-trial treatment. The highest corrosion resistance was observed for both A-78 V and S-78 V samples. The cytotoxicity assay revealed no changes in cell morphology or vitality. The MTT test proved comparable culture viability among all groups; however, the “S” samples showed statistically significantly higher fibroblast proliferation and adhesion scores compared to the “A” samples. Through the in vitro study, the low-pressure radiofrequency oxygen plasma treatment of the anodized Ti-6Al-4V alloy presented itself as an auspicious option in the field of transgingival element surface modification of implants.
Porous silicon gettering

We have studied a novel extrinsic gettering method that uses the large surface areas produced by a porous-silicon etch as gettering sites. The annealing step of the gettering used a high-flux solar furnace. We found that a high density of photons during annealing enhanced the impurity diffusion to the gettering sites. We used metallurgical-grade Si (MG-Si) prepared by directional solidification casting as the starting material. We propose to use porous-silicon-gettered MG-Si as a low-cost epitaxial substrate for polycrystalline silicon thin-film growth for solar cells.
Study of electromagnetic processes with the dielectron spectrometer HADES

Dielectron production in pp and dp reactions at 1.25 A.GeV has been studied with the High Acceptance DiElectron Spectrometer (HADES) at GSI. Results obtained in inclusive and exclusive channels are shown, along with π+, π− and η production in pp reactions at 1.25 and 2.2 GeV. Perspectives of experiments with π− beams are outlined.
A model for spatial conflict

Two species compete for territory along their mutual boundary. The species are fairly matched and the result of conflict is the invasion by one of the species of territory held by the other. A simple stochastic model for this process is described and rules are given for the calculation, as a function of time, of the probabilities that individual territories and groups of territories are held by a single species. Asymptotic results are given for the pattern of territories held by a single species, and here a remarkable distinction is seen between the cases of one-dimensional and two-dimensional competition and the case of three-dimensional competition. The process of invasion is contrasted with two relatively benign processes, that in which an exchange of territories is arranged and that in which a spatial alternation of species may be beneficial to the community. The implications of the long-term behaviour of such processes are discussed. It is suggested further that, under certain ideal conditions, it may be possible to estimate the duration of a spatial struggle for life by observing at some time the configuration of territories held by each species.
Development and Preliminary Application of a Droplet Digital PCR Assay for Quantifying the Oncolytic Herpes Simplex Virus Type 1 in the Clinical-Grade Production

Oncolytic herpes simplex virus (oHSV) is a type of virus that selectively targets and kills cancer cells, leaving normal cells unharmed. Accurate viral titer is of great importance for the production and application of oHSV products. Droplet digital PCR (ddPCR) is known for having good reproducibility, not requiring a standard curve, not being affected by inhibitors, and being precise even in the detection of low copies. In the present study, we developed a droplet digital PCR assay for the quantification of HSV-1 and applied it in the oHSV production. The established ddPCR showed good specificity, linearity, a low limit of quantification, great reproducibility, and accuracy. The quantification result was well-associated with that of plaque assay and CCID50. Amplification of the purified virus without DNA extraction by ddPCR presented similar results to that from the extracted DNA, confirming the good resistance against PCR inhibitors. With the ddPCR, viral titer could be monitored in real time during the production of oHSV; the optimal harvest time was determined for the best virus yield in each batch. The ddPCR can be used as a useful tool for the quantification of oHSV and greatly facilitate the manufacturing process of oHSV products.