Miracle-dz/UniFAR-FTUs huggingface dataset:
Circular RNA DGKB Promotes the Progression of Neuroblastoma by Targeting miR-873/GLI1 Axis

Accumulated evidences suggested that circular RNAs (circRNA) played critical roles in tumorigenesis and progression. To our knowledge, no study reported the function of circular RNA DGKB (circDGKB, circRNA ID: hsa_circ_0133622) on progression of neuroblastoma (NB). Here, we showed that circDGKB was upregulated in NB tissues compared to the normal dorsal root ganglia. Moreover, the expression level of circDGKB was negatively correlated with the survival rate of NB patients. Mechanically, overexpression of circDGKB promoted the proliferation, migration, invasion, and tumorigenesis of NB cells and reduced cell apoptosis, and vice versa. In addition, qRT-PCR and/or Western blot results showed that circDGKB overexpression inhibited the expression level of miR-873 and enhanced GLI1 expression. Moreover, miR-873 functioned an opposite role to circDGKB and significantly weakened circDGKB role in promoting NB progression. Furthermore, GLI1 upregulation also rescued the miR-873 role in inhibiting NB progression. In conclusion, our work proved that circDGKB promoted NB progression via targeting miR-873/GLI1 axis in vitro and in vivo. Our study provided a new target for NB treatment and indicated that circDGKB could act as a novel diagnostic marker for NB.
Individual differences in foraging decisions: information-gathering strategies or flexibility?

Information on where to find food patches, their quality, and food variance can have implications for fitness and survival when a current food patch fails. Individuals have been found to vary in their response to changes in food availability, and this has been related to several personality traits in animals such as exploration behavior that measures activity in a novel environment. We examined if personality-related variation in reactions to food availability change could be explained by information-gathering strategies (IGSs), where individuals vary in investing in sampling known patches as a trade-off to seeking new patches. We also examined if these relationships can be explained by an alternative hypothesis where individuals are expected to express variation in behavioral flexibility (BF). The BF hypothesis predicted that individuals rely more on either internal/prior or external/current information. In addition to a standardized exploration behavior test, we designed a new 5-day-long experiment where individual reactions to changes in food availability were measured using wild great tits (Parus major). We found that slow exploring individuals sampled empty food patches more than fast exploring individuals, supporting the IGS hypothesis. We found no evidence for personality-related differences in feeder choice in response to changes in food availability, nor personality-related differences in flexibility in behavioral responses.
Interferon-γ induced PD-L1 expression and soluble PD-L1 production in gastric cancer

Programmed death-ligand 1 (PD-L1) plays an essential role in tumor cell escape from anti-tumor immunity in various types of cancer, including gastric cancer (GC). The present study investigated the intracellular and membrane-bound expression of PD-L1 in the GC cell lines MKN1, MKN74, KATO III and OCUM-1. Furthermore, soluble PD-L1 (sPD-L1) level in the supernatant of GC cells and the serum of patients with GC and healthy controls was determined by ELISA. Interferon (IFN)-γ treatment of cells resulted in increased cytoplasmic expression of PD-L1 in GC cells in a dose-dependent manner, except for MKN74 cells; however, there was no association between tumor necrosis factor-α treatment and enhanced PD-L1 expression. Concordant with these findings, results from flow cytometry analysis demonstrated that membrane-bound PD-L1 expression was also increased following GC cell treatment with IFN-γ in a dose-dependent manner. In addition, significant sPD-L1 overproduction was observed only in the culture supernatant of OCUM-1 cells. Serum level of sPD-L1 was significantly increased in patients with GC, in particular in stage IV patients, compared with healthy controls. In conclusion, the present study demonstrated that IFN-γ treatment increased the intracellular and membrane-bound PD-L1 expression in GC cells. In addition, sPD-L1 was detected not only in the supernatant of GC cells but also in the serum of patients with GC. Further investigation on the underlying mechanism of regulation of PD-L1 expression and sPD-L1 production is required.
Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats (Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome

Little is known about skin microbiota in the context of the disease white-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans (Pd), that has caused enormous declines of hibernating North American bats over the past decade. Interestingly, some hibernating species, such as the big brown bat (Eptesicus fuscus), appear resistant to the disease and their skin microbiota could play a role. However, a comprehensive analysis of the skin microbiota of E. fuscus in the context of Pd has not been done. In January 2017, we captured hibernating E. fuscus, sampled their skin microbiota, and inoculated them with Pd or sham inoculum. We allowed the bats to hibernate in the lab under controlled conditions for 11 weeks and then sampled their skin microbiota to test the following hypotheses: (1) Pd infection would not disrupt the skin microbiota of Pd-resistant E. fuscus; and (2) microbial taxa with antifungal properties would be abundant both before and after inoculation with Pd. Using high-throughput 16S rRNA gene sequencing, we discovered that beta diversity of Pd-inoculated bats changed more over time than that of sham-inoculated bats. Still, the most abundant taxa in the community were stable throughout the experiment. Among the most abundant taxa, Pseudomonas and Rhodococcus are known for antifungal potential against Pd and other fungi. Thus, in contrast to hypothesis 1, Pd infection destabilized the skin microbiota but consistent with hypothesis 2, bacteria with known antifungal properties remained abundant and stable on the skin. This study is the first to provide a comprehensive survey of skin microbiota of E. fuscus, suggesting potential associations between the bat skin microbiota and resistance to the Pd infection and WNS. These results set the stage for future studies to characterize microbiota gene expression, better understand mechanisms of resistance to WNS, and help develop conservation strategies.
Commodity risk assessment of Jasminum polyanthum plants from Israel

Abstract The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation EU/2018/2019 as ‘High risk plants, plant products and other objects’. This Scientific Opinion covers all plant health risks posed by unrooted cuttings of Jasminum polyanthum produced in a protected environment (greenhouse) that are imported from Israel, taking into account the available scientific information, including the technical information provided by the NPPO of Israel by 15 March 2020. The relevance of an EU quarantine pest for this opinion was based on evidence that: (i) the pest is present in Israel; (ii) Jasminum is a host of the pest; and (iii) the pest can be associated with the commodity. The relevance of any other pest, not regulated in the EU, was based on evidence that: (i) the pest is present in Israel; (ii) the pest is absent in the EU; (iii) Jasminum is a host of the pest; (iv) the pest can be associated with the commodity and (v) the pest may have an impact and can pose a potential risk for the EU territory. Six species, the EU‐quarantine pest Scirtothrips dorsalis, and the EU non‐regulated pests Aonidiella orientalis, Milviscutulus mangiferae, Paracoccus marginatus, Pulvinaria psidii and Colletotrichum siamense fulfilled all relevant criteria and were selected for further evaluation. For these pests, the risk mitigation measures proposed in the technical dossier from Israel were evaluated taking into account the possible limiting factors. For these pests, an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on the pest, including uncertainties associated with the assessment. The estimated degree of pest freedom varies among the pests evaluated, with S. dorsalis being the pest most frequently expected on the imported plants. The Expert Knowledge Elicitation indicated, with 95% certainty, that between 9,958 and 10,000 bags per 10,000 would be free of S. dorsalis.
Systemic inflammatory indices predict tumor response to neoadjuvant chemoradiotherapy for locally advanced rectal cancer

Systemic inflammatory responses are associated with the prognosis of patients with colorectal cancer. However, the value in predicting tumor responses to neoadjuvant chemoradiotherapy (nCRT) remains to be elucidated. The current study aimed to investigate the association between systemic inflammatory indices and pathological complete response (pCR). The training and validation cohorts included 225 and 96 patients with locally advanced rectal cancer. The neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio were recorded prior to nCRT and radical surgery. Univariate and multivariate analysis were used to investigate the association between systemic inflammatory indices and pCR. Systemic inflammatory indices prior to or following treatment had no significant association with pCR; however, the percentage change in NLR from pre-nCRT to post-nCRT was associated with a poor response, and a percentage change of >21.5% NLR (P=0.006; OR=0.413; 95% CI=0.22–0.773) was a predictor of poor pCR. Therefore, in rectal cancer, the percentage change in NLR from pre- to post-nCRT was found to be a predictor of poor pCR.
Azo Dye Decolourisation using Crude Peroxidase from Armoracia rusticana Hairy Roots

Aim: The objective of the present work was to assess the ability of crude peroxidase from hairy roots ofArmoracia rusticana(horseradish) to decolourise two model azo dyes: The mono -azo dye Methyl Orange (MO) and the diazo dye Bismarck Brown (BB). Study Design: The enzymatic decolourisation of aqueous solutions of the model dyes was performed by varying reaction parameters like pH of reaction mixture, crude enzyme concentration, dye concentration and hydrogen peroxide concentration ; at ambient temperature (25±2∫C). The emphasis was on using a crude extract that showed high enzyme activity, despite being obtained by minimum processing, and virtually no OriginalResearch Article
Intestinal Inflammation Induced by Soybean Meal Ingestion Increases Intestinal Permeability and Neutrophil Turnover Independently of Microbiota in Zebrafish

Intestinal inflammation is a condition shared by several intestinal chronic diseases, such as Crohn's disease and ulcerative colitis, with severely detrimental consequences in the long run. Current mammalian models have considerably increased understanding of this pathological condition, highlighting the fact that, in most of the cases, it is a highly complex and multifactorial problem and difficult to deal with. Thus, there is an increasingly evident need for alternative animal models that could offer complementary approaches that have not been exploited in rodents, thereby contributing to a different view on the disease. Here, we report the effects of a soybean meal–induced intestinal inflammation model on intestinal integrity and function as well as on neutrophil recruitment and microbiota composition in zebrafish. We find that the induced intestinal inflammation process is accompanied by an increase in epithelial permeability in addition to changes in the mRNA levels of different tight junction proteins. Conversely, there was no evidence of damage of epithelial cells nor an increase in their proliferation. Of note, our results show that this intestinal inflammatory model is induced independently of the presence of microbiota. On the other hand, this inflammatory process affects intestinal physiology by decreasing protein absorption, increasing neutrophil replacement, and altering microbiota composition with a decrease in the diversity of cultivable bacteria.
Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts

Decomposition of animal bodies in the burial environment plays a key role in the biochemistry of the soil, altering the balance of the local microbial populations present before the introduction of the carcass. Despite the growing number of studies on decomposition and soil bacterial populations, less is known on its effects on fungal communities. Shifts in the fungal populations at different post-mortem intervals (PMIs) could provide insights for PMI estimation and clarify the role that specific fungal taxa have at specific decomposition stages. In this study, we buried pig carcasses over a period of 1- to 6-months, and we sampled the soil in contact with each carcass at different PMIs. We performed metabarcoding analysis of the mycobiome targeting both the internal transcribed spacer (ITS) 1 and 2, to elucidate which one was more suitable for this purpose. Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs, and the alteration of the soil fungal signature even after 6 months post-burial, showing the inability of soil communities to restore their original composition within this timeframe. The results highlighted taxonomic trends associated with specific PMIs, such as the increase of the Mortierellomycota after 4- and 6-months and of Ascomycota particularly after 2 months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited number of taxa specifically associated with the carrion and not present in the control soil, showing that the major contributors to the recorded changes are originated from the soil and were not introduced by the carrion. As this is the first study conducted on burial graves, it sets the baseline for additional studies to investigate the role of fungal communities on prolonged decomposition periods and to identify fungal biomarkers to improve the accuracy of PMI prediction for forensic applications.
Cryopreservation of Sheep Produced Embryos – Current and Future Perspectives

Due to scientific technologies are less commercially applied than in other animal species. However, it is very clear that, in the near future, those techniques are expected to have a central role in animal production as a consequence of genetic and reproductive demands. One drawback is that results obtained after sheep embryo cryopreservation are unattractive for commercial purposes. It is expected that a successful cryopreservation of sheep embryos can push forward all other reproductive biotechnologies in this species, such as multiple ovulation and embryo transfer (MOET), artificial insemination, or in vitro production of embryos. This paper tries to discuss the current and future perspectives of cryopreservation of in vivo - and in vitro -produced sheep embryos concerning advantages and limitations for its practical use and possible solutions for improving methods to allow a higher survival rate of cryopreserved embryos.
Cut-enhanced PolyCube-maps for feature-aware all-hex meshing

Volumetric PolyCube-Map-based methods offer automatic ways to construct all-hexahedral meshes for closed 3D polyhedral domains, but their meshing quality is limited by the lack of interior singularities and feature alignment. In the presented work, we propose cut-enhanced PolyCube-Maps, to introduce essential interior singularities and preserve most input features. Our main idea is simple and intuitive: by inserting proper parameterization seams into the initial PolyCube-Map via novel PolyCube cutting operations, the mapping distortion can be reduced significantly. The cut-enhanced PolyCube-Map computation includes feature-aware PolyCube-Map construction and cut-enhanced PolyCube deformation. The former aims to preserve input feature edges during the initial PolyCube-Map construction. The latter introduces seams into the volumetric PolyCube shape by cutting it through selective PolyCube edges and deforms the modified PolyCube under the seamless constraints to compute a low-distortion PolyCube-Map. The hexahedral mesh induced by the final PolyCube-Map can be further enhanced by our mesh improvement algorithm. We validate the efficacy of our method on a collection of more than one hundred CAD models and demonstrate its advantages over other automatic all-hex meshing methods and padding strategies. The limitations of cut-enhanced PolyCube-Maps are also discussed thoroughly.
Why the Cosmological Constant Seems to Hardly Care About Quantum Vacuum Fluctuations: Surprises From Background Independent Coarse Graining

Background Independence is a sine qua non for every satisfactory theory of Quantum Gravity. If one tries to establish a corresponding notion of Wilsonian renormalization, or coarse graining, it presents a major conceptual and technical difficulty usually. In this paper, we adopt the approach of the gravitational Effective Average Action and demonstrate that, generically, coarse graining in Quantum Gravity and in standard field theories on a non-dynamical spacetime are profoundly different. By means of a concrete example, which, in connection with the cosmological constant problem, is also interesting in its own right, we show that the surprising and sometimes counterintuitive implications of Background Independent coarse graining are neither restricted to high energies nor to strongly non-perturbative regimes. In fact, while our approach has been employed in most studies of Asymptotic Safety, this particular ultraviolet behavior plays no essential role in the present context.
Data-driven extraction and composition of secondary dynamics in facial performance capture

Performance capture of expressive subjects, particularly facial performances acquired with high spatial resolution, will inevitably incorporate some fraction of motion that is due to inertial effects and dynamic overshoot due to ballistic motion. This is true in most natural capture environments where the actor is able to move freely during their performance, rather than being tethered to a fixed position. Normally these secondary dynamic effects are unwanted, as the captured facial performance is often retargeted to different head motion, and sometimes to completely different characters, and in both cases the captured dynamic effects should be removed and new secondary effects should be added. This paper advances the hypothesis that for a highly constrained elastic medium such as the human face, these secondary inertial effects are predominantly due to the motion of the underlying bony structures (cranium and mandible). Our work aims to compute and characterize the difference between the captured dynamic facial performance, and a speculative quasistatic variant of the same motion should the inertial effects have been absent. This is used to either subtract parasitic secondary dynamics that resulted from unintentional motion during capture, or compose such effects on top of a quasistatic performance to simulate a new dynamic motion of the actor's body and skull, either artist-prescribed or acquired via motion capture. We propose a data-driven technique that comprises complementary removal and synthesis networks for secondary dynamics in facial performance capture. We show how such a system can be effectively trained from a collection of acquired dynamic deformations under varying expressions where the actor induces rigid head motion from walking and running, as well as forced oscillatory body motion in a controlled setting by external actuators.
Example-driven virtual cinematography by learning camera behaviors

Designing a camera motion controller that has the capacity to move a virtual camera automatically in relation with contents of a 3D animation, in a cinematographic and principled way, is a complex and challenging task. Many cinematographic rules exist, yet practice shows there are significant stylistic variations in how these can be applied. In this paper, we propose an example-driven camera controller which can extract camera behaviors from an example film clip and re-apply the extracted behaviors to a 3D animation, through learning from a collection of camera motions. Our first technical contribution is the design of a low-dimensional cinematic feature space that captures the essence of a film's cinematic characteristics (camera angle and distance, screen composition and character configurations) and which is coupled with a neural network to automatically extract these cinematic characteristics from real film clips. Our second technical contribution is the design of a cascaded deep-learning architecture trained to (i) recognize a variety of camera motion behaviors from the extracted cinematic features, and (ii) predict the future motion of a virtual camera given a character 3D animation. We propose to rely on a Mixture of Experts (MoE) gating+prediction mechanism to ensure that distinct camera behaviors can be learned while ensuring generalization. We demonstrate the features of our approach through experiments that highlight (i) the quality of our cinematic feature extractor (ii) the capacity to learn a range of behaviors through the gating mechanism, and (iii) the ability to generate a variety of camera motions by applying different behaviors extracted from film clips. Such an example-driven approach offers a high level of controllability which opens new possibilities toward a deeper understanding of cinematographic style and enhanced possibilities in exploiting real film data in virtual environments.
Massively parallel rendering of complex closed-form implicit surfaces

We present a new method for directly rendering complex closed-form implicit surfaces on modern GPUs, taking advantage of their massive parallelism. Our model representation is unambiguously solid, can be sampled at arbitrary resolution, and supports both constructive solid geometry (CSG) and more unusual modeling operations (e.g. smooth blending of shapes). The rendering strategy scales to large-scale models with thousands of arithmetic operations in their underlying mathematical expressions. Our method only requires C0 continuity, allowing for warping and blending operations which break Lipshitz continuity. To render a model, its underlying expression is evaluated in a shallow hierarchy of spatial regions, using a high branching factor for efficient parallelization. Interval arithmetic is used to both skip empty regions and construct reduced versions of the expression. The latter is the optimization that makes our algorithm practical: in one benchmark, expression complexity decreases by two orders of magnitude between the original and reduced expressions. Similar algorithms exist in the literature, but tend to be deeply recursive with heterogeneous workloads in each branch, which makes them GPU-unfriendly; our evaluation and expression reduction both run efficiently as massively parallel algorithms, entirely on the GPU. The resulting system renders complex implicit surfaces in high resolution and at interactive speeds. We examine how performance scales with computing power, presenting performance results on hardware ranging from older laptops to modern data-center GPUs, and showing significant improvements at each stage.