Miracle-dz/UniFAR-FTUs huggingface dataset:
A Hybrid Chalcone Combining the Trimethoxyphenyl and Isatinyl Groups Targets Multiple Oncogenic Proteins and Pathways in Hepatocellular Carcinoma Cells

Small molecule inhibitors that can simultaneously inhibit multiple oncogenic proteins in essential pathways are promising therapeutic chemicals for hepatocellular carcinoma (HCC). To combine the anticancer effects of combretastatins, chalcones and isatins, we synthesized a novel hybrid molecule 3’,4’,5’-trimethoxy-5-chloro-isatinylchalcone (3MCIC). 3MCIC inhibited proliferation of cultured HepG2 cells, causing rounding-up of the cells and massive vacuole accumulation in the cytoplasm. Paxillin and focal adhesion plaques were downregulated by 3MCIC. Surprisingly, unlike the microtubule (MT)-targeting agent CA-4 that inhibits tubulin polymerization, 3MCIC stabilized tubulin polymers both in living cells and in cell lysates. 3MCIC treatment reduced cyclin B1, CDK1, p-CDK1/2, and Rb, but increased p53 and p21. Moreover, 3MCIC caused GSK3β degradation by promoting GSK3β-Ser9 phosphorylation. Nevertheless, 3MCIC inhibited the Wnt/β-catenin pathway by downregulating β-catenin, c-Myc, cyclin D1 and E2F1. 3MCIC treatment not only activated the caspase-3-dependent apoptotic pathway, but also caused massive autophagy evidenced by rapid and drastic changes of LC3 and p62. 3MCIC also promoted cleavage and maturation of the lysosomal protease cathepsin D. Using ligand-affinity chromatography (LAC), target proteins captured onto the Sephacryl S1000-C12-3MCIC resins were isolated and analyzed by mass spectrometry (MS). Some of the LAC-MS identified targets, i.e., septin-2, vimentin, pan-cytokeratin, nucleolin, EF1α1/2, EBP1 (PA2G4), cyclin B1 and GSK3β, were further detected by Western blotting. Moreover, both septin-2 and HIF-1α decreased drastically in 3MCIC-treated HepG2 cells. Our data suggest that 3MCIC is a promising anticancer lead compound with novel targeting mechanisms, and also demonstrate the efficiency of LAC-MS based target identification in anticancer drug development.
Uropathogenic Escherichia coli Suppresses the Host Inflammatory Response via Pathogenicity Island Genes sisA and sisB

ABSTRACT Extraintestinal pathogenic Escherichia coli can successfully colonize the urinary tract of the immunocompetent host. In part, this is accomplished by dampening the host immune response. Indeed, the sisA and sisB genes (shiA-like inflammation suppressor genes A and B) of uropathogenic E. coli strain CFT073, homologs of the Shigella flexneri SHI-2 pathogenicity island gene shiA, suppress the host inflammatory response. A double deletion mutant (ΔsisA ΔsisB) resulted in a hyperinflammatory phenotype in an experimental model of ascending urinary tract infection. The ΔsisA ΔsisB mutant not only caused significantly more inflammatory foci in the kidneys of CBA/J mice (P = 0.0399), but these lesions were also histologically more severe (P = 0.0477) than lesions observed in mice infected with wild-type CFT073. This hyperinflammatory phenotype could be suppressed to wild-type levels by in vivo complementation of the ΔsisA ΔsisB mutant with either the sisA or sisB gene in trans. The ΔsisA ΔsisB mutant was outcompeted by wild-type CFT073 during cochallenge infection in the bladder (P = 0.0295) at 48 h postinoculation (hpi). However, during cochallenge infections, we reasoned that wild-type CFT073 could partially complement the ΔsisA ΔsisB mutant. Consistent with this, the most significant colonization defect of the ΔsisA ΔsisB mutant in vivo was observed during independent challenge relative to wild-type CFT073, with attenuation of the mutant observed in the bladder (P < 0.0001) and kidneys (P = 0.0003) at 6 hpi. By 24 and 48 hpi, the ΔsisA ΔsisB mutant was no longer significantly attenuated in the bladder or kidneys, suggesting that the sisA and sisB genes may be important for suppressing the host immune response during the initial stages of infection.
Efficient digit-serial normal basis multipliers over GF(2/sup m/)

In this article, two efficient architectures for digit-serial normal basis (DSNB) multipliers over GF(2/sup m/) are presented. These two structures have the same gate count and time complexity. A straightforward implementation leaves gate redundancy in both of them. An algorithm which can considerably reduce the redundancy is also developed. Moreover, the proposed architectures are compared with the existing ones in terms of gate and time complexities.
NFS Proxies : Design , Implementation and Applications

We present the design, implementation , evaluation and applications of a Virtualized NFS system. In the current implementation of NFS, clients need to be aware of the physical distribution of servers and the locations of files they wish to access. Changes in server state cannot be performed transparent to clients and consequently issues like load balancing become non-trivial. Moreover when NFS is used in a wide area environment, performance and security are far from satisfactory. We address these issues by ‘virtualizing NFS’; a proxy is interposed between clients and servers that provides an interface to decentralized storage on the servers. We make use of the Click modular router to implement our interface,the VNFS-Proxy. The VNFS-Proxy presents to NFS clients a unified shared file volume with scalable bandwidth and capacity. We achieve an efficient virtualization by processing NFS packets within the kernel. Our results show that our design incurs minimal overhead, while transparently virtualizing NFS. We also demonstrate the utility of our proxy by building applications such as a cache, an encrypted file system and a meta-data querying system on the proxy. We achieve our virtualization and the applications with no changes to the NFS client or server implementations.
Transgenic Insecticidal Crops and Natural Enemies: A Detailed Review of Laboratory Studies

ABSTRACT This review uses a data-driven, quantitative method to summarize the published, peer-reviewed literature about the impact of genetically modified (GM) plants on arthropod natural enemies in laboratory experiments. The method is similar to meta-analysis, and, in contrast to a simple author-vote counting method used by several earlier reviews, gives an objective, data-driven summary of existing knowledge about these effects. Significantly more non-neutral responses were observed than expected at random in 75% of the comparisons of natural enemy groups and response classes. These observations indicate that Cry toxins and proteinase inhibitors often have non-neutral effects on natural enemies. This synthesis identifies a continued bias toward studies on a few predator species, especially the green lacewing, Chrysoperla cornea Stephens, which may be more sensitive to GM insecticidal plants (16.8% of the quantified parameter responses were significantly negative) than predators in general (10.9% significantly negative effects without C. cornea). Parasitoids were more susceptible than predators to the effects of both Cry toxins and proteinase inhibitors, with fewer positive effects (18.0%, significant and nonsignificant positive effects combined) than negative ones (66.1%, significant and nonsignificant negative effects combined). GM plants can have a positive effect on natural enemies (4.8% of responses were significantly positive), although significant negative (21.2%) effects were more common. Although there are data on 48 natural enemy species, the database is still far from adequate to predict the effect of a Bt toxin or proteinase inhibitor on natural enemies.
Efficient Simulation of Structural Faults for the Reliability Evaluation at System-Level

In recent technology nodes, reliability is considered a part of the standard design ¿ow at all levels of embedded system design. While techniques that use only low-level models at gate- and register transfer-level offer high accuracy, they are too inefficient to consider the overall application of the embedded system. Multi-level models with high abstraction are essential to efficiently evaluate the impact of physical defects on the system. This paper provides a methodology that leverages state-of-the-art techniques for efficient fault simulation of structural faults together with transaction-level modeling. This way it is possible to accurately evaluate the impact of the faults on the entire hardware/software system. A case study of a system consisting of hardware and software for image compression and data encryption is presented and the method is compared to a standard gate/RT mixed-level approach.
A Novel Multistage Image Registration Technique with Graph-based Region Descriptors

Bowen, Francis R. Ph.D., Purdue University, December 2013. A Novel Multistage Image Registration Technique Using Graph-based Region Descriptors. Major Professors: Eliza Y. Du and Jianghai Hu. Successful image alignment is an essential function for many image processing methods. The geometric and photometric variations between images adversely affect the ability for an algorithm to estimate the transformation parameters that relate the two images. Local deformations, lightning conditions, object obstructions, and perspective differences all contribute to the challenges faced by traditional registration techniques. In this work, a novel multistage registration approach is proposed that is resilient to view point differences, image content variations, and lighting conditions. The proposed method is demonstrated to be effective for registration scenarios involving images of a scene or object before and after a disaster. Robust registration is realized through the utilization of a novel region descriptor which couples the spatial and textural characteristics of invariant feature points. Clusters of invariant feature points are shown to provide more discriminative features than the traditional point descriptors. The multistage method is a hierarchy of registration approaches that takes advantage of feature, intensity and Fourier-based techniques. The three phases include a limited search window method that employs the proposed graph-based region descriptor, a comprehensive approach which fuses intensity and feature-based analysis, and an exhaustive search method which also utilizes the region descriptor. Each successive stage of the registration technique is evaluated through an effective similarity metric which determines subsequent action. The registration of aerial and street view images from pre and post disaster provide strong evidence that the proposed method estimates
Learning weighted naive Bayes with accurate ranking

Naive Bayes is one of most effective classification algorithms. In many applications, however, a ranking of examples are more desirable than just classification. How to extend naive Bayes to improve its ranking performance is an interesting and useful question in practice. Weighted naive Bayes is an extension of naive Bayes, in which attributes have different weights. This paper investigates how to learn a weighted naive Bayes with accurate ranking from data, or more precisely, how to learn the weights of a weighted naive Bayes to produce accurate ranking. We explore various methods: the gain ratio method, the hill climbing method, and the Markov chain Monte Carlo method, the hill climbing method combined with the gain ratio method, and the Markov chain Monte Carlo method combined with the gain ratio method. Our experiments show that a weighted naive Bayes trained to produce accurate ranking outperforms naive Bayes.
Parallel public transport system and its application in the evacuation of large-scale activities

ACP (Artificial societies, Computational experiments, and Parallel execution) approach is adopted by our method to build parallel public transport system (PPTS). The framework of PPTS is proposed and some components are analyzed. Two key steps in building up PPTS are discussed. The first is growing up artificial public transport system from bottom up using agent-based technology. The second is implementing schedule plans of public vehicles using cloud computing. One specific PPTS is established for Guangzhou 2010 Asian Games. Its effectiveness is verified and illustrated by comparing the traffic parameters between before and after the employment.
Effects of Re-Used Plastic Film Mulching on Soil Moisture and Water Use Efficiency in Hetao Area, China

Aiming at reducing agricultural pollution caused by plastic film and increasing soil moisture and water use efficiency (WUE), the field experiments were conducted to investigate the effects of re-used plastic film mulching on soil moisture, sunflower’s yield and water use efficiency by compared with new plastic film mulching and bare field in Hetao area, China. The results showed that, soil water of re-used film mulching increased at different degree. Compared with bare field and new film mulching, soi1 moisture of re-used film were higher significantly 1.5 percentage points in 0-100 cm, and especially 1.9 or 2.6 percentage points in 0-10 cm during sunflower’s growth stage. Soil water of re-used film was more than that of bare field 24.8 mm (in 2010) and 33.0 mm (in 2011) before seeding, and 21.6mm (in 2010) and 24.5mm (in 2011) at harvest when soil water was replenished to same level for each treatment before sowing. Meanwhile, the grain yield of re-used film was higher significantly than that of bare field 11.4% (in 2010) and 16.8% (in 2011), and WUE of re-used film was higher significantly 15.7% (in 2010) and 22.7% (in 2011) respectively, no significant with new film. So it was worth to apply re-used film to agriculture production for improving the soil moisture, enhancing water use efficiency and increasing the yield of sunflower. We suggest that the application of re-used film mulching is a suitable soil management practice for increase water and WUE in Hetao area or other areas with similar conditions.
[Vertebral metrics: application of a new mechanical instrument to evaluate the spinal column].

OBJECTIVE To present the results of the first application of the new technology - Vertebral Metrics - the analysis of the 3D position of the vertex of each spinous process in pregnant women. MATERIAL AND METHODS The Vertebral Metrics was applied to women without associated pathology in four stages of pregnancy (12, 20, 32, 37 weeks gestation). We applied univariate linear models. RESULTS We found that the differences that occur during pregnancy are more significant at the position y (anteroposterior). It was found also that there is a positive correlation between the biomechanical position of the vertex of each of the vertebrae with the homologous position of rest. DISCUSSION/CONCLUSION Through Vertebral Metrics innovative results could be obtained in analyzing biomechanics of the spine. A device that has different applications can be easily adopted in areas such as orthopedics, neurosurgery, pediatrics and rehabilitation. It should also be noted that this instrument is not exhausted in the sample of this research because it can be further applied to the general population.
The yeast silent information regulator Sir4p anchors and partitions plasmids

Circular plasmids containing telomeric TG1-3 arrays or the HMR E silencer segregate efficiently between dividing cells of the yeast Saccharomyces cerevisiae. Subtelomeric X repeats augment the TG1-3 partitioning activity by a process that requires the SIR2, SIR3, and SIR4 genes, which are also required for silencer-based partitioning. Here we show that targeting Sir4p to DNA directly via fusion to the bacterial repressor LexA confers efficient mitotic segregation to otherwise unstable plasmids. The Sir4p partitioning activity resides within a 300-amino-acid region (residues 950 to 1262) which precedes the coiled-coil dimerization motif at the extreme carboxy end of the protein. Using a topology-based assay, we demonstrate that the partitioning domain also retards the axial rotation of LexA operators in vivo. The anchoring and partitioning properties of LexA-Sir4p chimeras persist despite the loss of the endogenous SIR genes, indicating that these functions are intrinsic to Sir4p and not to a complex of Sir factors. In contrast, inactivation of the Sir4p-interacting protein Rap1p reduces partitioning by a LexA-Sir4p fusion. The data are consistent with a model in which the partitioning and anchoring domain of Sir4p (PAD4 domain) attaches to a nuclear component that divides symmetrically between cells at mitosis; DNA linked to Sir4p by LexA serves as a reporter of protein movement in these experiments. We infer that the segregation behavior of telomere- and silencer-based plasmids is, in part, a consequence of these Sir4p-mediated interactions. The assays presented herein illustrate two novel approaches to monitor the intracellular dynamics of nuclear proteins.
High-level Information Fusion for Constrained SMC Methods and Applications

Information Fusion is a field that studies processes utilizing data from various input sources, and techniques exploiting this data to produce estimates and knowledge about objects and situations. On the other hand, human computation is a new and evolving research area that uses human intelligence to solve computational problems that are beyond the scope of existing artificial intelligence algorithms. In previous systems, humans’ role was mostly restricted for analysing a finished fusion product; however, in the current systems the role of humans is an integral element in a distributed framework, where many tasks can be accomplished by either humans or machines. Moreover, some information can be provided only by humans not machines, because the observational capabilities and opportunities for traditional electronic (hard) sensors are limited. A source-reliability-adaptive distributed non-linear estimation method applicable to a number of distributed state estimation problems is proposed. The proposed method requires only local data exchange among neighbouring sensor nodes. It therefore provides enhanced reliability, scalability, and ease of deployment. In particular, by taking into account the estimation reliability of each sensor node at any point in time, it yields a more robust distributed estimation. To perform the Multi-Model Particle Filtering (MMPF) in an adaptive distributed manner, a Gaussian approximation of the particle cloud obtained at each sensor node, along with a weighted Consensus Propagation (CP)-based distributed data aggregation scheme, are deployed to dynamically re-weight the particle clouds. The filtering is a soft-data-constrained variant of multi-model particle filter, and is capable of processing both soft human-generated data and conventional hard sensory data. If permanent noise occurs in the estimation provided by a sensor node, due to either a faulty sensing device or misleading soft data, the contribution of that node in the weighted consensus process is immediately reduced in order to alleviate its effect on the estimation provided by the neighbouring nodes and the entire network. The robustness of the proposed source-reliability-adaptive distributed estimation method is demonstrated through simulation results for agile target tracking scenarios. Agility here refers to cases in which the observed dynamics of targets deviate from the given probabilistic characterization. Furthermore, the same concept is applied to model soft data constrained multiple-model Probability Hypothesis Density (PHD) filter that can track agile multiple targets with nonlinear dynamics, which is a challenging problem. In this case, a Sequential Monte CarloProbability Hypothesis Density (SMC-PHD) filter deploys a Random Set (RS) theoretic formulation, along with Sequential Monte Carlo approximation, a variant of Bayes filtering. In general, the performance of Bayesian filtering-based methods can be enhanced by using
Palette: Distributing tables in software-defined networks

In software-defined networks (SDNs), the network controller first formulates abstract network-wide policies, and then implements them in the forwarding tables of network switches. However, fast SDN tables often cannot scale beyond a few hundred entries. This is because they typically include wildcards, and therefore are implemented using either expensive and power-hungry TCAMs, or complex and slow data structures. This paper presents the Palette distribution framework for decomposing large SDN tables into small ones and then distributing them across the network, while preserving the overall SDN policy semantics. Palette helps balance the sizes of the tables across the network, as well as reduce the total number of entries by sharing resources among different connections. It copes with two NP-hard optimization problems: Decomposing a large SDN table into equivalent subtables, and distributing the subtables such that each connection traverses each type of subtable at least once. To implement the Palette distribution framework, we introduce graph-theoretical formulations and algorithms, and show that they achieve close-to-optimal results in practice.
A Novel Digital Coded Track Signal-ITRS Based on TVM430

With the developing of the high-speed railways, the requirement for railway signalling turns more and more strict. Came from France, the TVM430 signal has more information up to 27 bits digital word, with each bit corresponding to one of the 27 frequencies modulated onto the carrier frequency in the track circuits. The presence of a particular frequency indicates a "1" bit and lack of corresponds to a "0". But the slow demodulation is the biggest flaw for TVM430. To solve the above problems, we design a new digital coded track signal - Improved TVM430 Railway Signalling (ITRS). ITRS reduces the number of TVM430's modulation frequency while provides the same information capacity as TVM430. We also search for cycle generating polynomial, add parity checking to the important code - speed identification code. New frequency, amplitude and phase are defined for frequency modulated signals. ITRS performs better in information capacity, reliability and demodulation speed.
Do seasonal changes in metabolic rate facilitate changes in diving behaviour?

SUMMARY Macaroni penguins were implanted with data loggers to record heart rate (fh), abdominal temperature (Tab) and diving depth during their pre-moult trip (summer) and winter migration. The penguins showed substantial differences in diving behaviour between the seasons. During winter, mean and maximum dive duration and dive depth were significantly greater than during summer, but the proportion of dives within the calculated aerobic dive limit (cADL) did not change. Rates of oxygen consumption were estimated from fh. As winter progressed, the rate of oxygen consumption during dive cycles (sV̇O2DC) declined significantly and mirrored the pattern of increase in maximum duration and depth. The decline in sV̇O2DC was matched by a decline in minimum rate of oxygen consumption (sV̇O2min). When sV̇O2min was subtracted from sV̇O2DC, the net cost of diving was unchanged between summer and winter. We suggest that the increased diving capacity demonstrated during the winter was facilitated by the decrease in sV̇O2min. Abdominal temperature declined during winter but this was not sufficient to explain the decline in sV̇O2min. A simple model of the interactions between sV̇O2min, thermal conductance and water temperature shows how a change in the distribution of fat stores and therefore a change in insulation and/or a difference in foraging location during winter could account for the observed reduction in sV̇O2min and hence sV̇O2DC.