Miracle-dz/UniFAR-FTUs huggingface dataset:
The U-Box E3 Ubiquitin Ligase TUD1 Functions with a Heterotrimeric G α Subunit to Regulate Brassinosteroid-Mediated Growth in Rice

Heterotrimeric G proteins are an important group of signaling molecules found in eukaryotes. They function with G-protein-coupled-receptors (GPCRs) to transduce various signals such as steroid hormones in animals. Nevertheless, their functions in plants are not well-defined. Previous studies suggested that the heterotrimeric G protein α subunit known as D1/RGA1 in rice is involved in a phytohormone gibberellin-mediated signaling pathway. Evidence also implicates D1 in the action of a second phytohormone Brassinosteroid (BR) and its pathway. However, it is unclear how D1 functions in this pathway, because so far no partner has been identified to act with D1. In this study, we report a D1 genetic interactor Taihu Dwarf1 (TUD1) that encodes a functional U-box E3 ubiquitin ligase. Genetic, phenotypic, and physiological analyses have shown that tud1 is epistatic to d1 and is less sensitive to BR treatment. Histological observations showed that the dwarf phenotype of tud1 is mainly due to decreased cell proliferation and disorganized cell files in aerial organs. Furthermore, we found that D1 directly interacts with TUD1. Taken together, these results demonstrate that D1 and TUD1 act together to mediate a BR-signaling pathway. This supports the idea that a D1-mediated BR signaling pathway occurs in rice to affect plant growth and development.
A Study of Selected Properties and Applications of AlMgB14 and Related Composites: Ultra-Hard Materials

This research presents a study of the hardness, electrical, and thermal properties AlMgB{sub 14} containing Al{sub 2}MgO{sub 4} spinel. This research also investigated how much Al{sub 2}MgO{sub 4} spinel consistently forms with AlMgB{sub 14}, if AlMgB{sub 14} materials can be produced by hot isostatic pressing (HIP), what effects TiC and TiB{sub 2} have on this composite material, and the importance of mechanical alloying. Included also is a study of the variation in hardness measurements and how they relate to SI units. Heretofore, all ultra-hard materials (hardness > 40 GPA) have been found to be cubic in structure, electrical insulators, and expensive; the behavior of AlMgB{sub 14}, which in certain specimens and compositions can have hardness values greater than 40 GPa, is therefore quite unusual since it is non-cubic, conductive, and moderate in cost. This offers an opportunity to investigate the relationship between hardness, thermal, and electrical properties from a new perspective. The main purpose of this project was to characterize the different properties of the AlMgB{sub 14} materials and to demonstrate that this material can be made in bulk. The technologies used for this study include microhardness measurement techniques, scanning electron microscopy, energy dispersive spectroscopy, x-ray diffraction spectroscopy, x-ray diffraction spectroscopy at different temperatures, optical microscopy, thermomechanical analysis, differential thermal analysis, 4-point probe resistivity, density techniques, Seebeck Effect, and Hall Effect. This research may lead to use of this material for applications where high abrasion resistance along with electrical conduction is needed. Also this research gave more information about a material that could have a great impact on industrial applications.
Iridoid enriched fraction from Ajuga iva reduce cholesterolemia, triacylglycerolemia and increase the lecithin:cholesterol acyltransferase activity of rats fed a cholesterol-rich diet

Objective: In this study, we examined the effect of iridoid (I) derived from lyophilized aqueous extract of Ajuga iva on serum HDL2 and HDL3 compositions and lecithin:cholesterol acyltransferase (LCAT) activity, enzyme responsible for reverse cholesterol transport. Methods: Male Wistar rats (n=24) weighing 120Â±5 g were fed a diet containing 1% cholesterol-rich diet for 15 days. After this phase, the hypercholesterolemic (HC) rats were divided into groups fed the same diet and received or not doses (5, 10 or 15 mg/kg b.w by intraperitoneal injection) of iridoid for 15 days. Results: Compared to HC group, serum total cholesterol value was 1.4- and 1.2-fold lower in the I5-HC and I10-HC groups. C-HDL2 and C-HDL3 values were increased in the I5-HC, I10-HC and I15-HC groups (3.2- and 4-, 2.2- and 4.2-, and 3.2- and 8.7-fold, respectively). HDL2 amounts were 4-, 4- and 2.5-fold higher in the I5-HC, I10-HC and I15-HC groups. In HDL3, phospholipids contents were similar, whereas, unesterified cholesterol values were 3.3-, 2.8- and 3-fold higher in the I5-HC, I10-HC and I15-HC groups. In HDL2, cholesteryl esters contents were significantly higher in the groups treated with iridoid (p
Quantitative Assessment of Grapevine Wood Colonization by the Dieback Fungus Eutypa lata

Eutypa lata is a fungal pathogen causing severe dieback in vineyards worldwide. This fungus colonizes vines through pruning wounds, eventually causing a brown sectorial necrosis in wood as well as stunted vegetative growth. Several years may pass between infection and the expression of external symptoms, hindering the rapid evaluation of both grapevine cultivars susceptibility and E. lata variation in aggressiveness. We aimed to develop a rapid quantitative method for the assessment of wood colonization after inoculation of cuttings in controlled conditions. We used several grape cultivars varying in susceptibility in the vineyard and fungal isolates with different levels of aggressiveness to monitor wood colonization during a maximum period of 2 months. Re-isolation allowed demonstration of the effects of both cultivars and fungal isolates on the rate of wood colonization. We also developed a real-time PCR method that was efficient in measuring fungal biomass, which was found to be correlated with isolate aggressiveness based on foliar symptom severity. The real-time PCR approach appears to be a useful technology to evaluate grapevine susceptibility to E. lata, and could be adapted to other pathogens associated with grapevine trunk diseases.
Transcriptional regulation of human MAP2 gene in melanoma: role of neuronal bHLH factors and Notch1 signaling

Microtubule-associated protein 2 (MAP2), a neuron-specific protein, stabilizes microtubules and is critical for neurite outgrowth and dendrite development. Although MAP2 is widely used as a marker of neuronal differentiation, regulation of its transcription has not been investigated. We showed that MAP2 is frequently activated in human cutaneous melanoma. Here, we identified a 2.2 kb region that is sufficient for neuronal-specific expression in vitro and in vivo. Comparative analysis of the mouse, rat and human MAP2 promoter sequences showed the presence of a conserved bHLH factor binding sites. Electrophoretic mobility shift analysis, promoter mutagenesis and co-transfection experiments showed that NeuroD, a pro-neuronal differentiation factor, and Hairy and Enhancer of Split (HES1), a transcription repressor, are involved in the regulation of MAP2 promoter activity. Melanoma cells express both NeuroD and HES1. Chromatin immunoprecipitation showed that in metastatic melanoma cells N-box region of the MAP2 promoter is occupied by endogenous HES1. We show that the inhibition of Notch signaling, a regulator of HES1 gene expression, and/or shRNA knockdown of HES1 results in the upregulation of MAP2 promoter activity. Thus, our data suggest that Notch signaling, which is implicated in melanoma progression, and HES1 play a role in MAP2 gene regulation during melanoma progression.
Measuring oxygen levels in Caco-2 cultures

Purpose Measuring oxygen levels in three different systems of Caco-2 cell culture. Methods Caco-2 cells were cultured in three different systems, using conventional polystyrene 24-well plates, special 24-well gas permeable plates, or on membrane inserts in conventional plates. Optical sensor spots were used to measure dissolved O2 levels in these cultured cells over the course of 6 days under normoxia (143 mmHg) and for 6 hours under hypoxia (7 mmHg). Western blot analysis was used to determine the protein levels of hypoxia-inducible factor 1α (HIF-1α) in the different cultures. Results All culture systems displayed lower O2 levels over time than expected when cultured under normoxia conditions. On average, O2 levels reached as low as 25 mmHg in 24-well plates but remained at 97 and 117 mmHg in gas permeable plates and membrane inserts, respectively. Under hypoxia, 1 mL cell cultures equilibrated to 7 mmHg O2 within the first 60 minutes and dropped to 0.39 and 0.61 mmHg O2 in 24-well and gas permeable plates, respectively, after the 6-hour incubation period. Cultures in membrane inserts did not equilibrate to 7 mmHg by the end of the 6-hour incubation period, where the lowest O2 measurements reached 23.12 mmHg. Western blots of HIF-1α protein level in the whole cell lysates of the different Caco-2 cultures revealed distinct stabilization of HIF-1α after hypoxic incubation for 1, 2, and 4 hours in 24-well plates as well as gas permeable plates. For membrane inserts, notable HIF-1α was seen after 4 hours of hypoxic incubation. Conclusion Cellular oxygen depletion was achieved in different hypoxic Caco-2 culture systems. However, different oxygen levels comparing different culture systems indicate that O2 level should be carefully considered in oxygen-dependent experiments.
A game approach for cooperative spectrum sharing in cognitive radio networks

We consider the problem of cooperative spectrum sharing among primary users PUs and secondary users SUs in cognitive radio networks. In our system, each PU selects a proper set of SUs to serve as the cooperative relays for its transmission and in return, leases portion of channel access time to the selected SUs for their own transmission. PU decides how to select SUs and how much time it would lease to SUs, and the cooperative SUs decide their respective power levels in helping PU's transmission, which are proportional to their access times. We assume that both PUs and SUs are rational and selfish. In single-PU scenario, we formulate the problem as a noncooperative game and prove that it converges to a unique Stackelberg equilibrium. We also propose an iterative algorithm to achieve the unique equilibrium point. We then extend the proposed cooperative mechanism to a multiple-PU scenario and develop a heuristic algorithm to assign proper SUs to each PU considering both performance and fairness. The simulation results show that when the competition among SUs is fierce, the performance gap between our heuristic algorithm and the optimal one is smaller than 3%. Copyright © 2013 John Wiley & Sons, Ltd.
Eco-Aware Online Power Management and Load Scheduling for Green Cloud Datacenters

Many of today's cloud datacenters are powered by electricity generated from brown energy (e.g., fuel fossil and oil), which directly translates into severe harm to the environment. To reduce the carbon footprint and the operating cost of datacenters, there is a clear trend to migrate to green datacenters, which are entirely (or partially) powered by renewable energy. However, given a portfolio with multiple off- and on-site power supplies (such as power grid, renewables, and batteries), it is challenging for datacenter operators to conduct efficient power management and thus meet the highly dynamic user demand. In this paper, we proposed an online algorithm, which is called EcoPower, to perform eco-aware power management and load scheduling jointly for geographically distributed cloud datacenters. Our objective is to minimize the time-average eco-aware power cost of cloud datacenters while still ensuring the quality-of-experience (QoE) constraint of user requests. To this end, we formulated the problem into a constrained stochastic optimization problem and apply the Lyapunov optimization theory to design an online control algorithm, which approaches the optimality with explicitly provable upper bounds. We also conducted extensive trace-driven simulations, and our results show that our proposed EcoPower algorithm can achieve a good balance between power cost savings, environment protection, and the user QoE, with the eco-aware power cost being cut down by over 20%. We found that wind dominant, solar complementary is a better strategy for cloud datacenters to integrate renewables into their power supply.
Diversity of Endophytic Fungi Associated with the Roots of Four Aquatic Plants Inhabiting Two Wetlands in Korea

Abstract A total of 4 aquatic plants, Eleocharis kuroguwai Ohwi, Hydrocharis dubia Backer, Salvinia natans All. , and Zizania latifolia Turcz. , were sampled from representative two wetlands of South Korea. A total of 38 endophytic fungal strains were isolated from aquatic plants native to the Daepyeong wetland, and 27 strains were isolated from the Jilnal wetland. The internal transcribed spacer regions of fungal isolates were sequenced and a phylogenetic analysis was performed. In addition, endophytic fungal diversity from each wetland and host plant species was deduced. A total of 25 fungal genera were purely isolated, and 16 fungal genera were isolated from each of the two wetlands. Commonly isolated genera from both wetlands were Aspergillus, Cladosporium, Clonostachys, Fusarium, Leptosphaeria, Penicillium, and Talaromyces. This study revealed that fungal diversity varied with environmental conditions and by host plant in representative two wetlands.
Variation of mechanical properties of high RRR and reactor grade niobium with heat treatments

Superconducting rf cavities used as accelerating structures in particle accelerators are made from high purity niobium with residual resistance ratios greater than 250. Reactor grade niobium is also used to make wave-guide and/or end group components for these accelerating structures. The major impurities in this type of niobium are interstitially dissolved gases such as hydrogen, nitrogen, and oxygen in addition to carbon. After fabricating the niobium accelerating structures, they are subjected to heat treatments for several hours in vacuum at temperatures of up to 900 C for degassing hydrogen or up to 1400 C for improving the thermal conductivity of niobium considerably. These heat treatments are affecting the mechanical properties of niobium drastically. In this paper the variation of the mechanical properties of high purity and reactor grade niobium with heat treatments in a vacuum of {approx} 10{sup -6} Torr and temperatures from 600 C to 1250 C for periods of 10 to 6 hours are presented.
Physical replicas and the Bose glass in cold atomic gases

We study cold atomic gases in a disorder potential and analyse the correlations between different systems subjected to the same disorder landscape. Such independent copies with the same disorder landscape are known as replicas. While, in general, these are not accessible experimentally in condensed matter systems, they can be realized using standard tools for controlling cold atomic gases in an optical lattice. Of special interest is the overlap function which represents a natural order parameter for disordered systems and is a correlation function between the atoms of two independent replicas with the same disorder. We demonstrate an efficient measurement scheme for the determination of this disorder-induced correlation function. As an application, we focus on the disordered Bose–Hubbard model and determine the overlap function within the perturbation theory and a numerical analysis. We find that the measurement of the overlap function allows for the identification of the Bose-glass phase in certain parameter regimes.
Improved multi-objective clustering algorithm using particle swarm optimization

Multi-objective clustering has received widespread attention recently, as it can obtain more accurate and reasonable solution. In this paper, an improved multi-objective clustering framework using particle swarm optimization (IMCPSO) is proposed. Firstly, a novel particle representation for clustering problem is designed to help PSO search clustering solutions in continuous space. Secondly, the distribution of Pareto set is analyzed. The analysis results are applied to the leader selection strategy, and make algorithm avoid trapping in local optimum. Moreover, a clustering solution-improved method is proposed, which can increase the efficiency in searching clustering solution greatly. In the experiments, 28 datasets are used and nine state-of-the-art clustering algorithms are compared, the proposed method is superior to other approaches in the evaluation index ARI.
5-HTTLPR Polymorphism Impacts Task-Evoked and Resting-State Activities of the Amygdala in Han Chinese

Background Prior research has shown that the amygdala of carriers of the short allele (s) of the serotonin transporter (5-HTT) gene (5-HTTLPR) have a larger response to negative emotional stimuli and higher spontaneous activity during the resting state than non-carriers. However, recent studies have suggested that the effects of 5-HTTLPR may be specific to different ethnic groups. Few studies have been conducted to address this issue. Methodology/Principal Findings Blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) was conducted on thirty-eight healthy Han Chinese subjects (l/l group, n = 19; s/s group, n = 19) during the resting state and during an emotional processing task. Compared with the s/s group, the l/l group showed significantly increased regional homogeneity or local synchronization in the right amygdala during the resting state (|t|>2.028, p<0.05, corrected), but no significant difference was found in the bilateral amygdala in response to negative stimuli in the emotional processing task. Conclusions/Significance 5-HTTLPR can alter the spontaneous activity of the amygdala in Han Chinese. However, the effect of 5-HTTLPR on the amygdala both in task state and resting state in Asian population was no similar with Caucasians. They suggest that the effect of 5-HTTLPR on the amygdala may be modulated by ethnic differences.
Using constraint propagation and domain reduction for the generation phase in declarative modeling

This paper presents an oriented object constraint solver based on constraint propagation and domain reduction for the generation phase in declarative modeling. The solver supports generic constraints and heterogeneous parameters via generic domains. This ensures adaptability and efficiency of the resolution process in complex cases. As an application, a declarative system for 3D environment planning is presented.
Improvement of an Automatic Speech Recognition Toolkit

The Kaldi toolkit provides a library of modules designed to expedite the creation of automatic speech recognition systems for research purposes. For purposes of acoustic modelling, the toolkit provides a framework for training Neural networks by stochastic gradient descent. Recent research, however, indicates that other standard nonlinear optimization techniques offer speed improvements and simplification of the training process. In this paper we build and test modules compatible with the toolkit to implement alternative training methods. 1 The Automatic Speech Recognition Pipeline The entire automatic speech recognition pipeline serves to convert a segment of spoken word audio (known as an utterance) to a corresponding accurate transcript. For our purposes we can break the automatic speech-to-text transcription process into several key functional blocks: Feature extraction, acoustic modelling, and decoding. Figure 1: ASR Pipeline 1.1 Feature extraction During feature extraction, windows of raw PCM audio samples are transformed into features that better represent the speech content of the signal within that window. This is most often accomplished by use of Mel-frequency cepstral coefficients (MFCCs). These coefficients are derived from the spectrum of the frequency domain, representing the change in frequency content of the speech signal. The frequency domain is mapped nonlinearly so as to approximate human sensitivity to differences in pitch. Consequently, each window of n audio samples comprises a “frame” that can be described by a feature vector of its n coefficients. Given an utterance m frames in duration, calculation of MFCC features will result in a matrix of features of dimension m× n. Other methods, such as PCA whitening, may then be used to transform and reduce this feature space. 1.2 Acoustic modelling An acoustic model serves to map the extracted features to a sequence of likely spoken sounds, known as phonemes. In particular, this is accomplished by using a sliding window over the frames of feature data, and then employing a statistical model to predict the probability that the central frame of the window is a result of any given phoneme being spoken. As such, the acoustic model ultimately associates each frame of audio with a distribution over the phonemes.
Lentiviral Vectors Mediate Long-Term and High Efficiency Transgene Expression in HEK 293T cells

Objectives:Lentiviral vectors have been used successfully to rapidly produce decigram quantities of active recombinant proteins in mammalian cell lines. To optimize the protein production platform, the roles of Ubiquitous Chromatin Opening Element (UCOE), an insulator, and selected promoters were evaluated based on efficiency and stability of foreign gene expression mediated by lentiviral vectors. Methods: Five lentiviral vectors, pFIN-EF1α-GFP-2A-mCherH-WPRE containing EF1α promoter and HS4 insulator, p'HR.cppt. 3'1.2kb-UCOE-SFFV-eGFP containing SFFV promoter and UCOE, pTYF-CMV(β-globin intron)-eGFP containing CMV promoter and β-globin intron, pTYF-CMV-eGFP containing CMV promoter, and pTYF-EF1α-eGFP with EF1α promoter were packaged, titered, and then transduced into 293T cells (1000 viral genomes per cell). The transduced cells were passaged once every three days at a ratio of 1:10. Expression level and stability of the foreign gene, green fluorescence protein (GFP), was evaluated using fluorescent microscopy and flow cytometry. Furthermore, we constructed a hepatitis C virus (HCV) E1 recombinant lentiviral vector, pLV-CMV-E1, driven by the CMV promoter. This vector was packaged and transduced into 293T cells, and the recombinant cell lines with stable expression of E1 protein were established by limiting dilution. Results:GFP expression in 293T cells transduced with the five lentiviral vectors peaked between passages 3 and 5 and persisted for more than 5 weeks. The expression was prolonged in the cells transduced with TYF-CMV (β-globin intron)-eGFP or TYF-CMV-eGFP, demonstrating less than a 50% decrease even at 9 weeks post transduction (p>0.05). The TYF-CMV-eGFP-transduced cells began with a higher level of GFP expression than other vectors did. The percentage of GFP positive cells for any of the five lentiviral vectors sustained over time. Moreover, the survival rates of all transfected cells exceeded 80% at both 5 and 9 weeks post transduction. Surprisingly, neither the HS4 insulator nor the UCOE sequence improved the GFP expression level or stability. Clonal cell lines with HCV E1 gene were generated from LV-CMV-E1 vector-infected 293T cells. A representative recombinant cell line maintained stable E1expression for at least 9 weeks without significant difference in morphology compared with untreated 293T cells. Conclusion: The results suggest that all five vectors can stably transduce 293T cells, producing long term transgene expression with different efficiencies. However, neither the insulator nor the UCOE improved the GFP expression. The vectors containing the promoter CMV or CMV (β-globin intron) generated the highest gene expressions, manifesting as more favorable candidates for recombinant protein production in HEK293T cells.