Miracle-dz/UniFAR-FTUs huggingface dataset:
Generalized Gradient Equivariant Multivalued Maps, Approximation and Degree

Consider the Euclidean space Rn with the orthogonal action of a compact Lie group G. We prove that a locally Lipschitz G-invariant mapping f from Rn to R can be uniformly approximated by G-invariant smooth mappings g in such a way that the gradient of g is a graph approximation of Clarkes generalized gradient of f. This result enables a proper development of equivariant gradient degree theory for a class of set-valued gradient mappings.
Thermo-optic phase shifter with sub-microsecond switching time and low power consumption

We propose a thermo-optic phase shifter utilizing multimode interference in a silicon waveguide. The electrodes were attached to the section where the multimode interference had the minimum optical electric field around the sidewalls. We designed the multimode waveguide width to reduce optical propagation loss in the C–L wavelength band (1.53–1.625 μm). We succeeded in developing a low optical loss thermo-optic phase shifter with less than 0.1 dB in the wavelength range of 1.5 to 1.6 μm. Moreover, wavelength dependence was reduced by adjusting the number of electrodes. An optical switch with the designed thermo-optic phase shifter was fabricated and used to estimate the optical switching time. Switching time of several microseconds was obtained by normal pulse operation, and ultrafast optical switching of about 500 ns was realized by overdrive control.
Combination of Mesenchymal Stem Cell-Delivered Oncolytic Virus with Prodrug Activation Increases Efficacy and Safety of Colorectal Cancer Therapy

Although oncolytic viruses are currently being evaluated for cancer treatment in clinical trials, systemic administration is hindered by many factors that prevent them from reaching the tumor cells. When administered systemically, mesenchymal stem cells (MSCs) target tumors, and therefore constitute good cell carriers for oncolytic viruses. MSCs were primed with trichostatin A under hypoxia, which upregulated the expression of CXCR4, a chemokine receptor involved in tumor tropism, and coxsackievirus and adenovirus receptor that plays an important role in adenoviral infection. After priming, MSCs were loaded with conditionally replicative adenovirus that exhibits limited proliferation in cells with a functional p53 pathway and encodes Escherichia coli nitroreductase (NTR) enzymes (CRAdNTR) for targeting tumor cells. Primed MSCs increased tumor tropism and susceptibility to adenoviral infection, and successfully protected CRAdNTR from neutralization by anti-adenovirus antibodies both in vitro and in vivo, and specifically targeted p53-deficient colorectal tumors when infused intravenously. Analyses of deproteinized tissues by UPLC-MS/QTOF revealed that these MSCs converted the co-administered prodrug CB1954 into cytotoxic metabolites, such as 4-hydroxylamine and 2-amine, inducing oncolysis and tumor growth inhibition without being toxic for the host vital organs. This study shows that the combination of oncolytic viruses delivered by MSCs with the activation of prodrugs is a new cancer treatment strategy that provides a new approach for the development of oncolytic viral therapy for various cancers.
C19ORF66 broadly escapes viral-induced endonuclease cleavage and restricts Kaposi’s Sarcoma Associated Herpesvirus (KSHV)

One striking characteristic of certain herpesviruses is their ability to induce rapid and widespread RNA decay in order to gain access to host resources. This phenotype is induced by viral endoribonucleases, including SOX in KSHV, muSOX in MHV68, BGLF5 in EBV and vhs in HSV-1. Here, we performed comparative RNA-seq upon expression of these herpesviral endonucleases in order to characterize their effect on the host transcriptome. Consistent with previous reports, we found that approximately two thirds of transcripts are downregulated in cells expressing any of these viral endonucleases. Among transcripts spared from degradation, we uncovered a cluster of transcripts that systematically escape degradation from all tested endonucleases. Among these escapees, we identified C19ORF66 and reveal that like the previously identified escapees, this transcript is protected from degradation by its 3’UTR. We then show that C19ORF66, a known anti-viral protein, is a potent KSHV restriction factor, suggesting that its ability to escape viral cleavage may be an important component of the host response to viral infection. Collectively, our comparative approach is a powerful tool to pinpoint key regulators of the viral-host interplay and led us to uncover a novel KSHV regulator.
Adaptive fault estimation observer design for switched systems with actuator and sensor faults

In this paper, the problem of fault estimation for continuous-time switched system with actuator and sensor faults is investigated. Firstly, based on the average dwell-time method and switched Lyapunov function, a fault estimation observer is designed for the augmented switched system, which can ensure that the error system is asymptotically stable with an H ∞ performance index. Next, an algorithm is proposed to realize fault estimation accurately. Finally, an example is given to illustrate the effectiveness of the designed methods.
DBN-DNN: discrimination and classification of VNG sequence using deep neural network framework in the EMD domain

ABSTRACT The Vestibulo-ocular response VOR is characterized by a smooth pursuit eye movements in one direction, called slow phase of ocular nystagmus, interrupted by resetting saccades fast phase of nystagmus in the other direction. Recording of ocular nystagmus during vestibular tests does not quantify the true response of the vestibulo-ocular reflex (VOR). In order to extract the real VOR, our study is focused on nystagmus analysis using videonystagmography (VNG) technique based on measuring amplitude vibration of eyeball movement. The effectiveness of this attendance is severely topic to the attention and the experience of ENT doctors. In this case, automatic methods of image analysis offer the possibility of obtaining a homogeneous, objective and above all fast diagnosis of vestibular disorder. In this paper, a fully automatic system based on nystagmus parameter analysis using a pupil detection algorithm is proposed. After a segmentation stage, a deep neural Network based classification method is applied on 90 eye movement recordings from videonystagmography (VNG) containing two types of peripheral vestibular disorders and normal patients. Experimental results obtained after several simulation, show the efficiency of the proposed methodology when compared with other classification methods.
Characteristics of Fluorescence Spectra, UV Spectra, and Specific Growth Rates during the Outbreak of Toxic Microcystis Aeruginosa FACHB-905 and Non-Toxic FACHB-469 under Different Nutrient Conditions in a Eutrophic Microcosmic Simulation Device

Microcystis aeruginosa is the dominant alga forming cyanobacteria blooms, the growth of which is limited by available nutrients. Thus, it is necessary to study cyanobacteria blooms and explore the growth of Microcystis aeruginosa under different nutrient conditions. In this paper, we take Microcystis aeruginosa, including toxic Freshwater Algae Culture of Hydrobiology Collection (FACHB)-905 and non-toxic FACHB-469 strains, into account. The strains were cultured using a simulation device under different nutrient conditions. Ultraviolet spectra, three-dimensional fluorescence spectra, and kinetic parameter indicators of the two species are studied. Compared to FACHB-469, the results show that the specific growth rate of FACHB-905 is much higher, in particular, FACHB-905 is the dominant species under low nutrient conditions. Furthermore, the UV spectral characteristics indicate that the molecular weight of dissolved organic matter in the culture tank of toxic FACHB-905 is greater than that of FACHB-469. Additionally, the humification index of toxic FACHB-905 is slightly higher as well, which suggests that it is more stable in the presence of dissolved organic matter during blooms. Therefore, the toxic Microcystis strain is more likely to become the dominant species in water blooms under lower eutrophic conditions and water blooms formed by the toxic Microcystis strain may be more difficult to recover from.
Optimizing execution for pipelined‐based distributed deep learning in a heterogeneously networked GPU cluster

Exorbitant resources (computing and memory) are required to train a deep neural network (DNN). Often researchers deploy an approach that uses distributed parallel training to acquire larger models faster on GPUs. This approach has its detriments, though; on one hand, a GPU's expanded capacity to compute also produces bigger bottlenecks in inter‐GPU's communications during model training, and multi‐GPU systems lead to complex connectivity. Workload schedulers then end up having to consider hardware topology and requirements for workload communication, in hopes of allocating GPU resources to optimize execution time and improve usage in a heterogeneous environment. On the other hand, the high memory requirements to train a DNN model make running the training processes on GPUs onerous. To contend with this, we introduce two execution optimization methods based on pipeline‐hybrid parallelism (using both data and model parallelism) in a GPU cluster with heterogeneous networking. First, we propose a model partition algorithm that accelerates pipeline‐hybrid parallelism training between heterogeneously network‐connected GPUs. Second, we introduce a cost‐balanced recomputing algorithm to reduce memory usage in the pipeline mode. Experiments show that our solution (Pipe‐Torch) averages a speedup of 1.4× compared with data parallelism, and reduces the memory footprint while maintaining pipelined load‐balanced training.
Fault diagnosis of key components in the rotating machinery based on Fourier transform multi-filter decomposition and optimized LightGBM

Rotating machinery is a primary element of mechanical equipment, and thus fault diagnosis of its key components is very important to improve the reliability and safety of modern industrial systems. The key point to diagnose the faults of these components is to extract effectively the hidden fault information. However, the actual vibration signals of rotating machinery have nonlinear and non-stationary characteristics, so traditional signal decomposition methods are unable to extract the frequency components accurately, leading to spectrum overlap of the decomposed sub-signals. Therefore, a rotating machinery fault diagnosis approach based on Fourier transform multi-filter decomposition (FTMFD), fuzzy entropy (FE), joint mutual information maximization (JMIM), and a light gradient boosting machine (LightGBM), is proposed in this paper. FTMFD is used to extract the frequency domain information of the raw vibration signals, whereas FE is used to calculate and extract the fault information of the decomposed sub-signals. Then feature selection is carried out by using JMIM to reduce the influence of redundant features on data analysis and classification accuracy. Furthermore, LightGBM is used to rank the candidate features and outputs the fault diagnosis result. Experimental results from two real datasets show that the proposed method achieves higher accuracy with fewer features than some existing methods for fault recognition. Various working conditions are also considered and verified.
Bootstrapped inference for variance parameters, measures of heterogeneity and random effects in multilevel logistic regression models

We used Monte Carlo simulations to assess the performance of three bootstrap procedures for use with multilevel data (the parametric bootstrap, the residuals bootstrap, and the nonparametric bootstrap) for estimating the sampling variation of three measures of cluster variation and heterogeneity when using a multilevel logistic regression model: the variance of the distribution of the random effects, the variance partition coefficient (equivalent here to the intraclass correlation coefficient), and the median odds ratio. We also described a novel parametric bootstrap procedure to estimate the standard errors of the predicted cluster-specific random effects. Our results suggest that the parametric and residuals bootstrap should, in general, be used to estimate the sampling variation of key measures of cluster variation and heterogeneity. The performance of the novel parametric bootstrap procedure for estimating the standard errors of predicted cluster-specific random effects tended to exceed that of the model-based estimates.
A Method for Identifying and Countering HID Attacks - Virus Detection in BMP Images

The aim of the article - develop a method for protecting modern systems from attacks using BMP image files and HID attacks. This article describes the features of BMP format images. The method of injecting computer viruses in BMP image and attacks in order to overcome the means of protection. The article suggests methods for detecting viruses in BMP image files and counteracting HID attacks. Developed programs demonstrate the effectiveness of protection against the considered attacks
Marker-assisted selection for scald (Rhynchosporium commune L.) resistance gene(s) in barley breeding for dry areas

Barley scald, caused by Rhynchosporium commune is one of the most prevalent diseases in barley (Hordeum vulgare L.) worldwide. The primary loss from scald is reduced yield, which can exceed 25% in dry areas. In our earlier studies, we developed a low-resolution linkage map for recombinant inbred lines of the cross Tadmor/WI2291. Quantitative trait loci (QTLs) for scald were localized on chromosomes 2H and 3H flanked by Simple Sequence Repeat (SSR) markers HVM54 and Bmac0093b on 2H and HVLTPP8, HVM62 and Bmag0006 on 3H. These chromosome 3H markers were found to be located close to the Rrs1 − R. commune resistance gene(s) on chromosome 3H. In this study, 10 homozygous resistant and 10 homozygous susceptible plants each from the F7 population of Tadmor/ Sel160, a panel of 23 barley varieties used routinely in the International Centre for Agricultural Research in the Dry Areas (ICARDA) breeding program and three populations were used for scald resistance screening using 25 DNA markers that are located very close to scald resistance gene(s) on barley chromosomes. Only five of those markers clearly discriminated co-dominantly between resistant and susceptible plants. These markers, Ebmac0871SSR, HVS3-SCAR, Bmag0006-SSR, reside on different arms of barley chromosome 3H. Ebmac871 is localized on the short arm of 3H and HVS3 and Bmag0006 are localized on the long arm of 3H. This result indicates that the scald resistance genes which they tag are probably close to the centromeric region of this chromosome. Scald resistance from several sources map to the proximal region of the long arm of chromosome 3H, forming the complex Rrs1 locus. The availability of highly polymorphic markers for the discrimination of breeding material would be extremely useful for barley breeders to select for the trait at the DNA level rather than relying on phenotypic expression and infection reaction.
Comprehensive effects of exogenous salicylic acid and light on chlorophyll fluorescence parameters and photosynthetic oxygen evolution in Ulva prolifera

Ulva prolifera is one of the causative species of green tides. Salicylic acid (SA) alleviated the high-temperature damage by up-regulating a portion of antioxidant-related proteins, however, little is understood regarding the impacts of SA under high light in this species. In order to study the regulation effects of SA on U. prolifera under different light conditions, we grew this species under three SA concentrations (0, 2.5, 5.0 µg mL-1) and three light levels [high light (HL): 400 μmol(photon) m-2 s-1, medium light (ML): 160 μmol(photon) m-2 s-1, and low light (LL): 70 μmol(photon) m-2 s-1]. After 3 d, the growth, chlorophyll fluorescence parameters, photosynthetic oxygen rate production, and superoxide dismutase (SOD) activity of U. prolifera were investigated. We found that: (1) The relative growth rate (RGR) of U. prolifera increased with the increase of light, no matter if with or without SA; under the three light levels, the highest RGR was observed in the presence of 2.5 µg(SA) mL-1. (2) U. prolifera grown under HL conditions showed the highest values in nonphotochemical quenching and total content of cartenoids. (3) Under three light levels, the dark respiration rate, the net, maximal, and gross photosynthetic oxygen rate significantly decreased by SA. (4) The highest value of SOD activity was observed under LL in the presence of SA (5.0 µg mL-1). In conclusion, the effects of light on the physiology in U. prolifera could be mediated by SA in a concentration-dependent manner.
Molecular evolution across developmental time reveals rapid divergence in early embryogenesis

Ontogenetic development hinges on the changes in gene expression in time and space within an organism, suggesting that the demands of ontogenetic growth can impose or reveal predictable pattern in the molecular evolution of genes expressed dynamically across development. Here we characterize co-expression modules of the C. elegans transcriptome, using a time series of 30 points from early-embryo to adult. By capturing the functional form of expression profiles with quantitative metrics, we find fastest evolution in the distinctive set of genes with transcript abundance that declines through development from a peak in young embryos. These genes are highly enriched for oogenic function (maternal provisioning), are non-randomly distributed in the genome, and correspond to a life stage especially prone to inviability in inter-species hybrids. These observations conflict with the “early conservation model” for the evolution of development, though expression-weighted sequence divergence analysis provides some support for the “hourglass model. ” Genes in co-expression modules that peak toward adulthood also evolve fast, being hyper-enriched for roles in spermatogenesis, implicating a history of sexual selection and relaxation of selection on sperm as key factors driving rapid change to ontogenetically distinguishable co-expression modules of genes. We propose that these predictable trends of molecular evolution for dynamically-expressed genes across ontogeny predispose particular life stages, early embryogenesis in particular, to hybrid dysfunction in the speciation process. Impact Summary The development of an organism from a single-celled embryo to a reproductive adult depends on dynamic gene expression over developmental time, with natural selection capable of shaping the molecular evolution of those differentially-expressed genes in distinct ways. We quantitatively analyzed the dynamic transcriptome profiles across 30 timepoints in development for the nematode C. elegans. In addition to rapid evolution of adult-expressed genes with functional roles in sperm, we uncovered the unexpected result that the distinctive set of genes that evolve fastest are those with peak expression in young embryos, conflicting with some models of the evolution of development. The rapid molecular evolution of genes in early embryogenesis contrasts with the exceptional conservation of embryonic cell lineages between species, and corresponds to a developmental period that is especially sensitive to inviability in inter-species hybrid embryos. We propose that these predictable trends of molecular evolution for dynamically-expressed genes across development predispose particular life stages, early embryogenesis in particular, to hybrid dysfunction in the speciation process.
Different groups of ground‐dwelling spiders share similar trophic niches in temperate forests

Generalistic interactions between predator and prey may vary with ecosystem type, predator traits, and prey traits, but the interplay of these factors has not been assessed in ground food webs. We investigated trophic interactions of ground‐dwelling spiders across eight forests in European Russia associated with body size, hunting strategy, microhabitat specialization, potential prey type, potential prey population density, and forest type (coniferous vs. broadleaved). We analyzed 128 individual spiders, including juveniles, all identified to the family level with two complementary methods: molecular gut content analysis, and stable isotope analysis of carbon and nitrogen. The results suggest that feeding frequency of spiders is affected by predator body size and by selection of certain prey type. Stable isotope analysis showed similar trophic niches among spider families, varying moderately with forest type. Larger spiders had higher Δ13C values than smaller ones, but similar Δ15N values, suggesting that different size classes of spiders belong to different food chains. Results based on stable isotope and molecular gut content analyses were weakly linked, indicating them targeting different trophic niche dimensions. At least for the group‐level interactions, family identity and hunting strategy of predator has little predictive power while predator body size and prey traits affected trophic niche dimensions calling for future studies in this direction. Large spiders feed more and rely on different basal resources than small spiders, suggesting that including small species and juveniles provides a more comprehensive picture of food web organization.
Recent research of feeding practices and the nutrition of lactating dairy goats*

ABSTRACT Dairy goats can mobilize considerable body fat for support of milk production, but this can necessitate a high nutritional plane later for replenishment. Tissue mobilization during gestation should be controlled so as not to impair lactational performance. Dairy goats can markedly vary feeding behaviour in response to factors such as restricted periods of access; however, further studies are needed to address the efficiency of production. With some tolerance of goats to plant secondary metabolites and voluntary consumption of a wide array of materials, regionally available byproducts and other nonconventional feedstuffs can be used to minimize production costs. Dairy goats are resilient to moderately harsh environmental conditions, but more extreme ones should be addressed with anticipated future climate change. Some differences in the effects of dietary inclusion of fats and oils between dairy goats and cattle may relate to ruminal microbial conditions as well as the susceptibility of mammary gland enzymes to bioactive conjugated linoleic acid isomers. Much research is being conducted to improve the fatty acid composition of fat in goat milk in regard to effects on human health through the use of fats and oils as well as plant secondary metabolites, and effects on antioxidant status are increasingly being considered as well.