Miracle-dz/UniFAR-FTUs huggingface dataset:
NIR-to-visible upconversion nanoparticles for fluorescent labeling and targeted delivery of siRNA

Near-infrared (NIR)-to-visible upconversion fluorescent nanoparticles were synthesized and used for imaging and targeted delivery of small interfering RNA (siRNA) to cancer cells. Silica-coated NaYF4 upconversion nanoparticles (UCNs) co-doped with lanthanide ions (Yb/Er) were synthesized. Folic acid and anti-Her2 antibody conjugated UCNs were used to fluorescently label the folate receptors of HT-29 cells and Her2 receptors of SK-BR-3 cells, respectively. The intracellular uptake of the folic acid and antibody conjugated UCNs was visualized using a confocal fluorescence microscope equipped with an NIR laser. siRNA was attached to anti-Her2 antibody conjugated UCNs and the delivery of these nanoparticles to SK-BR-3 cells was studied. Meanwhile, a luciferase assay was established to confirm the gene silencing effect of siRNA. Upconversion nanoparticles can serve as a fluorescent probe and delivery system for simultaneous imaging and delivery of biological molecules.
GUI Interaction Testing: Incorporating Event Context

Graphical user interfaces (GUIs), due to their event-driven nature, present an enormous and potentially unbounded way for users to interact with software. During testing, it is important to “adequately cover” this interaction space. In this paper, we develop a new family of coverage criteria for GUI testing grounded in combinatorial interaction testing. The key motivation of using combinatorial techniques is that they enable us to incorporate “context” into the criteria in terms of event combinations, sequence length, and by including all possible positions for each event. Our new criteria range in both efficiency (measured by the size of the test suite) and effectiveness (the ability of the test suites to detect faults). In a case study on eight applications, we automatically generate test cases and systematically explore the impact of context, as captured by our new criteria. Our study shows that by increasing the event combinations tested and by controlling the relative positions of events defined by the new criteria, we can detect a large number of faults that were undetectable by earlier techniques.
Second-order networks, gambling, and corruption on Indian mobile phone networks

This article explores unintended effects of recent growth in India’s mobile phone network. Using a case study of the Indian Premier League (IPL) – a popular cricket league that has encouraged mobile phone usage among fans – this article argues that India’s large and inclusive mobile phone networks have enabled significant new gambling and corruption. The spatial possibilities of mobile networks have led to new organizational forms in gambling and corruption, with small-scale local activity increasingly supplanted by organized syndicates located in Mumbai and Dubai. Based on interviews with mobile phone users and participants in betting rings, this article shows that the IPL mobile network enables second-order networks of criminal activity by making it easier to administer illegal action and easier to escape detection. This article emphasizes three ways that mobile networks facilitate gambling. First, their functionality, portability, and near-universality allow for new flows of information and capital. Second, mobile networks allow for new scale and new organizational forms, allowing a shift from local bookies to national and international syndicates. Third, mobile networks have dramatically enlarged the gambling sector in India. These changes have helped turn cricket gambling into a global industry with India at its center.
On the probability distribution of busy virtual channels

A major issue in modelling the performance merits of interconnection network is dealing with virtual channels. Some analytical models chose not to deal with this issue at all i.e. one virtual channel per physical channel. More sophisticated models, however, relayed on a method proposed by Dally to capture the effect of arranging the physical channel into many virtual channels. In this study, we investigate the accuracy of Dally's method and propose an alternative approach to deal with virtual channels in analytical performance modelling. The new method is validated via simulation experiments and results reveal its accuracy under different traffic conditions
MiRNA-155 promotes the invasion of colorectal cancer SW-480 cells through regulating the Wnt/β-catenin.

OBJECTIVE To investigate the role of microRNA-155 (miR-155) in the potential invasion of colon cancer cell and the underlying mechanism. PATIENTS AND METHODS The expression level of miR-155 in colon cancer and adjacent normal tissues was detected by Real-time quantitative polymerase chain reaction (RT-PCR). miR-155 mimics (miR-155), or siRNA against β-catenin (β-catenin siRNA), was transfected into human colon cancer cell line SW-480 using Lipofectamine 2000, respectively. RT-PCR was used to measure the expression levels of miR-155 and β-catenin mRNA, and β-catenin protein expression level was detected by Western blot. The in-vitro cell invasion abilities were determined by transwell invasion assays after up-regulating miR-155 or knocking down of β-catenin. RESULTS MiR-155 directly regulates β-catenin at the transcriptional level, and promotes the invasion potential of colon cancer cell, at least partly through the upregulation of β-catenin. CONCLUSIONS The findings of this study suggest that miR-155 and β-catenin may have a unique potential as a novel biomarker candidate for diagnosis and treatment of tumor metastasis.
Fuzzy Logic Based QoS Optimization Mechanism for Service Composition

Increase emphasis on Quality of Service and highly changing environments make management of composite services a time consuming and complicated task. Adaptation approaches aim to mitigate the management problem by adjusting composite services to the environment conditions, maintaining functional and quality levels, and reducing human intervention. This paper presents an adaptation approach that implements self-optimization based on fuzzy logic. The proposed optimization model performs service selection based on the analysis of historical and real QoS data, gathered at different stages during the execution of composite services. The use of fuzzy inference systems enables the evaluation of the measured QoS values, helps deciding whether adaptation is needed or not, and how to perform service selection. Experimental results show significant improvements in the global QoS of the use case scenario, providing reductions up to 20.5% in response time, 33.4% in cost and 31.2% in energy consumption.
Topical application of hPDGF-A-modified porcine BMSC and keratinocytes loaded on acellular HAM promotes the healing of combined radiation-wound skin injury in minipigs

Purpose: To evaluate the efficacy of cultured cutaneous substitute (CCS) in accelerating the healing of combined radiation-skin wound injury (CRWI) in minipigs. Material and methods: Autologous porcine bone marrow-derived mesenchymal stem cells (BMSC) and skin-derived keratinocytes (SK) were infected by recombinant retrovirus expressing human (h) platelet-derived growth factor-A (hPDGF-A). CCS was constructed by loading acellular human amniotic membrane (HAM) with normal porcine BMSC and SK (BMSC−/SK−CCS) or with hPDGF-A modified counterparts (BMSC+/SK+CCS). The expression of exogenous hPDGF-A in cells and CCS was assessed by reverse transcription polymerase chain reaction (RT-PCR) and enzyme linked immunosorbent assay (ELISA). The CCS or HAM were grafted to the dorsal CRWI sites (20 Gy local irradiation plus full-thickness skin removal, diameter = 40 mm) of minipigs. Wound healing rate and pathological changes were observed. Results: High levels of hPDGF-A expression were confirmed in gene-modified cells (3780 pg/ml), cultured CCS (506 pg/ml) and transplanted CCS (250 pg/ml). The transplantation of the BMSC+/SK+CCS resulted in a shorter healing time (16–18, days) (P < 0.05 vs. other groups). The healing rates ranked as BMSC+/SK+CCS > BMSC−/SK−CCS > HAM > wound control. Pathologically, there were better granulation formation and re-epithelialisation, and collagen deposition in BMSC+/SK+CCS-treated wound than those in other groups. The angiogenesis ability followed the same order as healing rate of different groups. At day 7, the area densities of vasculature in granulation tissue of group BMSC+/SK+CCS, BMSC−/SK−CCS, HAM, wound only were 15.4, 10.3, 6.0 and 5.7%, respectively, while the number densities of vasculature was 767, 691, 126 and 109 (number/mm2), respectively. Conclusions: Topical transplantation of hPDGF-A modified CCS may be applicable to the management of refractory wounds.
A framework for network aware caching for video on demand systems

Video on Demand (VoD) services allow users to select and locally consume remotely stored content. We investigate the use of caching to solve the scalability issues of several existing VoD providers. We propose metrics and goals that define the requirements of a caching framework for CDNs of VoD systems. Using data logs collected from Motorola equipment from Comcast VoD deployments we show that several classic caching solutions do not satisfy the proposed goals. We address this issue by developing novel techniques for predicting future values of several metrics of interest. We rely on computed predictions to define the penalty imposed on the system, both network and caching sites, when not storing individual items. We use item penalties to devise novel caching and static content placement strategies. We use the previously mentioned data logs to validate our solutions and show that they satisfy all the defined goals.
Efficient Representation and Fusion of Hybrid Joint Densities for Clusters in Nonlinear Hybrid Bayesian Networks

Undirected cycles in Bayesian networks are often treated by using clustering methods. This results in networks with nodes characterized by joint probability densities instead of marginal densities. An efficient representation of these hybrid joint densities is essential especially in nonlinear hybrid net works containing continuous as well as discrete variables. In this article we present a unified representation of continuous, discrete, and hybrid joint densities. This representation is based on Gaussian and Dirac mixtures and allows for analytic evaluation of arbitrary hybrid networks without loosing structural in formation, even for networks containing clusters. Furthermore we derive update formulae for marginal and joint densities from a system theoretic point of view by treating a Bayesian network as a system of cascaded subsystems. Together with the presented mixture representation of densities this yields an exact analytic updating scheme
High-Speed OTDM and WDM Networks Using Traveling-Wave Electroabsorption Modulators

We describe the design and performance of a number of elements based on traveling-wave electroabsorption modulators (TW-EAMs) in optical time-division-multiplexing (OTDM) and wavelength-division-multiplexing (WDM) networks. The incorporation of traveling-wave (TW) electrode design into electroabsorption modulators (EAMs) relieves the resistance-capacitance (RC ) bandwidth limitation common to lumped components, enabling higher operation speed without shortening the device. As a result, high-speed operation can be combined with essential modulator characteristics such as modulation efficiency and extinction ratio. While significant modulation bandwidth has been achieved, a lesser known aspect is that the TW electrode also provides an extra dimension for improving and enabling functionalities beyond broadband modulation. This new dimension originates from the distributed effect of the TW design and its interactions with distinctive EAM properties. This paper reviews such developments in recent years with specific applications for optical signal processing in OTDM and WDM networks. The covered functionalities include various optical gating operations for OTDM, regenerative wavelength conversions for WDM, and clock recovery
Inferential time-decaying Bloom filters

Time-Decaying Bloom Filters are efficient, probabilistic data structures used to answer queries on recently inserted items. As new items are inserted, memory of older items decays. Incorrect query responses incur penalties borne by the application using the filter. Most existing filters may only be tuned to static penalties, and they ignore Bayesian priors and information latent in the filter. We address these issues in an integrated way by converting existing filters into inferential filters. Inferential filters combine latent filter information with Bayesian priors to make query-specific optimal decisions. Our methods are applicable to any Bloom Filter, but we focus on developing inferential time-decaying filters, which support new query types and sliding window queries with varying error penalties. We develop the inferential version of the existing Timing Bloom Filter. Through experiments on real and synthetic datasets, we show that when penalties are query-specific and prior probabilities are known, the inferential Timing Bloom Filter reduces penalties for incorrect responses to sliding-window queries by up to 70%.
A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data

MOTIVATION Signaling pathways are dynamic events that take place over a given period of time. In order to identify these pathways, expression data over time are required. Dynamic Bayesian network (DBN) is an important approach for predicting the gene regulatory networks from time course expression data. However, two fundamental problems greatly reduce the effectiveness of current DBN methods. The first problem is the relatively low accuracy of prediction, and the second is the excessive computational time. RESULTS In this paper, we present a DBN-based approach with increased accuracy and reduced computational time compared with existing DBN methods. Unlike previous methods, our approach limits potential regulators to those genes with either earlier or simultaneous expression changes (up- or down-regulation) in relation to their target genes. This allows us to limit the number of potential regulators and consequently reduce the search space. Furthermore, we use the time difference between the initial change in the expression of a given regulator gene and its potential target gene to estimate the transcriptional time lag between these two genes. This method of time lag estimation increases the accuracy of predicting gene regulatory networks. Our approach is evaluated using time-series expression data measured during the yeast cell cycle. The results demonstrate that this approach can predict regulatory networks with significantly improved accuracy and reduced computational time compared with existing DBN approaches.
Aggregation algorithms for neural network ensemble construction

How to generate and aggregate base learners to have optimal ensemble generalization capabilities is an important questions in building composite regression/classification machines. We present here an evaluation of several algorithms for artificial neural networks aggregation in the regression settings, including new proposals and comparing them with standard methods in the literature. We also discuss a potential problem with sequential algorithms: the non frequent but damaging selection through their heuristics of particularly bad ensemble members. We show that one can cope with this problem by allowing individual weighting of aggregate members. Our algorithms and their weighted modifications are favorably tested against other methods in the literature, producing a performance improvement on the standard statistical databases used as benchmarks.
The Effect of Color on Automaticity of Aesthetic Judgments

The cognitive processing mode used to process color while making aesthetic judgments was examined. In two experiments, participants rated artistic photographs for preference. Half the participants performed a concurrent memory preload task while rating the photographs to index whether automatic or controlled modes of processing was engaged. Overall, the results showed that preload had little effect on the pattern of ratings for color, black and white, and false color versions of the photographs. The results suggest that color processing during the judgment task was automatic and required few cognitive resources. Furthermore, the results indicate that the dual-mode processing framework can be a useful theoretical tool for examining the cognitive processes that underlie aesthetic experience.
Spatiotemporal properties of layer V neurons of the rat primary somatosensory cortex.

Animals in their natural environments actively process spatiotemporally complex sensory signals in order to guide adaptive behavior. It therefore seems likely that the properties of both single neurons and neural ensembles should reflect the dynamic nature of such interactions. During exploratory behaviors, rats move their whiskers to actively discriminate between different tactile features. We investigated whether this dynamic sensory processing was reflected in the spatial and temporal properties of neurons in layer V of the 'whisker area' in the rat primary somatosensory cortex. We found that the majority of layer V neurons had large (8.5+/-4.9 whiskers) spatiotemporal receptive fields (i.e. individual cells responded best to different whiskers as a function of post-stimulus time), and that the excitatory responses of surround whiskers formed a spatial gradient of excitation that seemed to reflect the greater use of the ventral and caudal whiskers during natural behaviors. Analyses of ensembles of layer V neurons revealed that single-whisker stimuli activated a portion of layer V that extends well beyond a single cortical column (average of 5.6 barrel cortical columns). Based on these results, we conclude that the rat primary somatosensory cortex does not appear to operate as a static decoder of tactile information. On the contrary, our data suggest that tactile processing in rats is likely to involve the on-going interactions between populations of broadly tuned neurons in the thalamocortical pathway.
Probing the Dynamic Distribution of Bound States for Methylcytosine-binding Domains on DNA*

Background: Although highly homologous to MBD2, the functional role of MBD3 remains in question. Results: MBD3 preferentially localizes to methylated and, to a lesser degree, unmethylated CpG dinucleotides. Conclusion: Dynamic distribution between methylated and unmethylated sites modifies the genomic localization of MBD3. Significance: Changes in the dynamic distribution on DNA dictate functional differences between MBD proteins. Although highly homologous to other methylcytosine-binding domain (MBD) proteins, MBD3 does not selectively bind methylated DNA, and thus the functional role of MBD3 remains in question. To explore the structural basis of its binding properties and potential function, we characterized the solution structure and binding distribution of the MBD3 MBD on hydroxymethylated, methylated, and unmethylated DNA. The overall fold of this domain is very similar to other MBDs, yet a key loop involved in DNA binding is more disordered than previously observed. Specific recognition of methylated DNA constrains the structure of this loop and results in large chemical shift changes in NMR spectra. Based on these spectral changes, we show that MBD3 preferentially localizes to methylated and, to a lesser degree, unmethylated cytosine-guanosine dinucleotides (CpGs), yet does not distinguish between hydroxymethylated and unmethylated sites. Measuring residual dipolar couplings for the different bound states clearly shows that the MBD3 structure does not change between methylation-specific and nonspecific binding modes. Furthermore, residual dipolar couplings measured for MBD3 bound to methylated DNA can be described by a linear combination of those for the methylation and nonspecific binding modes, confirming the preferential localization to methylated sites. The highly homologous MBD2 protein shows similar but much stronger localization to methylated as well as unmethylated CpGs. Together, these data establish the structural basis for the relative distribution of MBD2 and MBD3 on genomic DNA and their observed occupancy at active and inactive CpG-rich promoters.
Quantification and localization of features in time-frequency plane

Many feature extraction techniques in literature have studied data representation, but most techniques do not explicitly investigate the feature localization aspect. This is one of the first works in which signals have been transformed to matrices using positive time-frequency transform, and matrix decomposition and representation techniques such as PCA, ICA, and NMF have been applied on these matrices to study the feature representation and localization issues. To estimate each techniquespsila localization, we propose a localization measurement method. We also construct a non stationary synthetic signal which resembles major characteristics of real world signals, and then apply the feature extraction techniques on a simple time-frequency distribution (TFD) of this signal. The localization results show that matrix factorization 1-D deconvolution (NMF1D) offers the most localized features with 99.6% localization. In addition, we demonstrate that under different number of basis components and noisy conditions, NMF1D offers the most robust localization.
Effect of Fibroblast Growth Factor 2 on Equine Synovial Fluid Chondroprogenitor Expansion and Chondrogenesis

Mesenchymal stem cells have been identified in the synovial fluid of several species. This study was conducted to characterize chondroprogenitor (CP) cells in equine synovial fluid (SF) and to determine the effect of fibroblast growth factor 2 (FGF-2) on SF-CP monolayer proliferation and subsequent chondrogenesis. We hypothesized that FGF-2 would stimulate SF-CP proliferation and postexpansion chondrogenesis. SF aspirates were collected from adult equine joints. Colony-forming unit (CFU) assays were performed during primary cultures. At first passage, SF-cells were seeded at low density, with or without FGF-2. Following monolayer expansion and serial immunophenotyping, cells were transferred to chondrogenic pellet cultures. Pellets were analyzed for chondrogenic mRNA expression and cartilage matrix secretion. There was a mean of 59.2 CFU/mL of SF. FGF-2 increased the number of population doublings during two monolayer passages and halved the population doubling times. FGF-2 did not alter the immunophenotype of SF-CPs during monolayer expansion, nor did FGF-2 compromise chondrogenesis. Hypertrophic phenotypic markers were not expressed in control or FGF-2 groups. FGF-2 did prevent the development of a “fibroblastic” cell layer around pellet periphery. FGF-2 significantly accelerates in vitro SF-CP expansion, the major hurdle to clinical application of this cell population, without detrimentally affecting subsequent chondrogenic capacity.
Intensity position modulation for free-space laser communication system

In this research a novel modulation technique for free-space laser communication system called Intensity Position Modulation (IPM) is carried out. According to TEM00 mode of a laser beam and by linear fitting on the Gaussian function as an approximation, the variation of linear part on the reverse biased pn photodiode produced alternating currents which contain the information. Here, no characteristic property of the beam as intensity or frequency is changed and only the beam position moves laterally. We demonstrated that in this method no bandwidth is required, so it is possible to reduce the background radiation noise by narrowband filtering of the carrier. The fidelity of the analog voice communication system which is made upon the IPM is satisfactory and we are able to transmit the audio signals up to 1Km.