Miracle-dz/UniFAR-FTUs huggingface dataset:
Chitosan/siRNA Nanoparticles Targeting Cyclooxygenase Type 2 Attenuate Unilateral Ureteral Obstruction-induced Kidney Injury in Mice

Cyclooxygenase type 2 (COX-2) plays a predominant role in the progression of kidney injury in obstructive nephropathy. The aim of this study was to test the efficacy of chitosan/small interfering RNA (siRNA) nanoparticles to knockdown COX-2 specifically in macrophages to prevent kidney injury induced by unilateral ureteral obstruction (UUO). Using optical imaging techniques and confocal microscopy, we demonstrated that chitosan/siRNA nanoparticles accumulated in macrophages in the obstructed kidney. Consistent with the imaging data, the obstructed kidney contained a higher amount of siRNA and macrophages. Chitosan-formulated siRNA against COX-2 was evaluated on RAW macrophages demonstrating reduced COX-2 expression and activity after LPS stimulation. Injection of COX-2 chitosan/siRNA nanoparticles in mice subjected to three-day UUO diminished the UUO-induced COX-2 expression. Likewise, macrophages in the obstructed kidney had reduced COX-2 immunoreactivity, and histological examination showed lesser tubular damage in COX-2 siRNA-treated UUO mice. Parenchymal inflammation, assessed by tumor necrosis factor-alpha (TNF-α) and interleukin 6 mRNA expression, was attenuated by COX-2 siRNA. Furthermore, treatment with COX-2 siRNA reduced heme oxygenase-1 and cleaved caspase-3 in UUO mice, indicating lesser oxidative stress and apoptosis. Our results demonstrate a novel strategy to prevent UUO-induced kidney damage by using chitosan/siRNA nanoparticles to knockdown COX-2 specifically in macrophages.
Measurement of the blood‐brain barrier permeability and leakage space using dynamic MR imaging. 1. Fundamental concepts

Leakage of Gd‐DTPA through a defective blood‐brain barrier is measured quantitatively using dynamic MRI scanning, in which repeated scans are made after a bolus injection. Image registration artifacts are minimized; a dose of 0.1 mM/kg and an IR sequence enable enhancement to be measured quantitatively. The triexponential enhancement curve is fitted to a theoretical model based on compartmental analysis. The transfer constant, or permeability surface area product per unit volume of tissue (k), and leakage space per unit volume of tissue (y) are measured. Estimates for a quickly enhancing multiple sclerosis lesion are k = 0.050 min−1, v1 = 21%; for a slow one k = 0.013 min−1, v1 = 49%. This implies permeability in the range 4‐17 × 10−6 cm s−1, in broad agreement with other physiological methods. The method is noninvasive and can be used to make serial measurements in patients and in experimental animal models. The time course of pathological aspects of diseases with blood‐brain barrier breakdown, such as multiple sclerosis, tumors, and infections (e.g., HIV) can be studied, along with their response to therapy. The measurements are of physiological variables and are therefore independent of imaging equipment and field. © 1991 Academic Press, Inc.
Utilising Stream Reasoning Techniques to Create a Self-Adaptation Framework for Cloud Environments

As cloud computing systems are reaching the stage where the human effort required to maintain them at an operational level is unsupportable, one of the major challenges faced by cloud computing providers is to develop appropriate mechanisms for run-time monitoring and adaptation, to prevent cloud platforms from quickly dissolving into a non-reliable environment. In this context, the application of intelligent approaches to Autonomic Clouds may offer promising opportunities. In this paper we present a novel approach to provide cloud platforms with autonomic capabilities based on utilising techniques from the domains of the Semantic Web and Stream Reasoning. The main idea of this approach is to encode values, monitored within cloud platforms, with Semantic Web languages, which will allow us to integrate these semantically enriched observation streams with static ontological knowledge and apply intelligent reasoning. Based on such run-time reasoning capabilities, we are able to perform analysis and failure diagnosis, and suggest further adaptation actions. As aninitial proof of concept, we sketch out a conceptual architecture for a self-adaptation framework and introduce a prototype solution implementing this architecture.
CO-MAP: Improving Mobile Multiple Access Efficiency With Location Input

Based on plenty of sensors on smartphones and tablets, their location information becomes more accurate and easy to access. Many position-based applications have thus been developed. As these mobile devices have become the main access approach of 802.11-based wireless local area networks (WLAN), location information also provides opportunities to improve the performance of underlying wireless communication. This paper presents CO-MAP (Co-Occurrence MAP), which leverages location information to handle exposed and hidden terminal problems, which are still a major cause of throughput degradation in mobile WLANs. With the positions of nodes, CO-MAP rapidly builds a co-occurrence map showing which two links can occur concurrently. Meanwhile, to avoid potential collisions, it selects the best settings of frame transmissions based on a novel analytic network model when hidden terminals are distinguished. CO-MAP improves the goodputs of both downlinks and uplinks in an instant and distributed manner. Our implementation on a hardware testbed demonstrates that CO-MAP can accurately detect potential interferers, and provide significant gain of goodput for both exposed and hidden terminal scenarios. The simulation results also suggest that imperfect position hints can still bring substantial improvement on the multiple access efficiency.
Cloud Technology for Mining Association Rules in Microarray Gene Expression Datasets

Microarray gene expression techniques and tools have become of a substantial importance and widely used to analyze the protein-protein interaction (PPI) and gene regulation network (GRN) research in recent years since it can capture the expressions of thousands of genes in a single experiment. Such dataset poses a great challenge for finding association rules in a faster way because of the presence of large number of columns but a small number of rows. Therefore, to meet the challenge of high volume of gene expression and the complexity of microarray data, various data mining methods and applications have been proposed for analyzing gene expressions. However, it is not trivial to extract biologically meaningful information from the huge amount of gene expression data in understanding of gene regulation networks and cellular state, because most cellular processes are regulated by changes in gene expression. Association rule mining techniques are helpful to find relationship between genes, but most of the developed association rule mining algorithms are based on main memory and single processor based techniques which are not capable of handling ever increasing large data and producing result in a faster way. In this paper, we proposed a MapReduce framework for mining association rules from a huge microarray gene expression dataset on Hadoop; which not only overcomes of the main memory bottleneck but also highly scalable in terms of increasing data size. When we apply this new method to the mice lungs and spinal cord microarray compendium data, it identifies a majority of known regulons as well as novel potential target genes of numerous key transcription factors. Extensive experimental results show that our proposed approach is efficient for mining high confident association rules from large microarray gene expression datasets in terms of time and scalability.
Proteolipid Protein Is Required for Transport of Sirtuin 2 into CNS Myelin

Mice lacking the expression of proteolipid protein (PLP)/DM20 in oligodendrocytes provide a genuine model for spastic paraplegia (SPG-2). Their axons are well myelinated but exhibit impaired axonal transport and progressive degeneration, which is difficult to attribute to the absence of a single myelin protein. We hypothesized that secondary molecular changes in PLPnull myelin contribute to the loss of PLP/DM20-dependent neuroprotection and provide more insight into glia-axonal interactions in this disease model. By gel-based proteome analysis, we identified >160 proteins in purified myelin membranes, which allowed us to systematically monitor the CNS myelin proteome of adult PLPnull mice, before the onset of disease. We identified three proteins of the septin family to be reduced in abundance, but the nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase sirtuin 2 (SIRT2) was virtually absent. SIRT2 is expressed throughout the oligodendrocyte lineage, and immunoelectron microscopy revealed its association with myelin. Loss of SIRT2 in PLPnull was posttranscriptional, suggesting that PLP/DM20 is required for its transport into the myelin compartment. Because normal SIRT2 activity is controlled by the NAD+/NADH ratio, its function may be coupled to the axo-glial metabolism and the long-term support of axons by oligodendrocytes.
A locality sensitive multi-module cache with explicit management

Cache memories are often inefficiently managed, which results in significant memory penalties. An important reason for this poor performance is the homogeneous management of all memory references, even though different memory references may exhibit a very different locality. In this work, we present a novel data cache architecture composed of different modules, each module exploiting a particular type of locality. The information of which module each fetched data is placed on is passed to the hardware by means of a hint encoded in the memory instructions. This hint is set based on a locality analysis that can be performed by the compiler or using profiling data. The proposed data cache organization exhibits a high-performance for numerical codes, even with low capacity, A SKI3 cache has a miss ratio that is about 0.4 times the miss ratio of an SKI3 direct-mapped cache and it is very close to that of a 64KB fullyassociative cache, when data prefetching is not considered. Furthermore, the locality analysis allows for a selective one-block lookahead prefetch scheme, just for those references that exhibit spatial locality. This prefetch firther reduces the miss ratio to one half of that of a 64KB fully-associative cache, with a negligible increase in memory traffic compared with the non-prefetching scheme, due to the locality-driven selective approach. Although the proposed data cache organization is oriented towards numerical codes, which usually suffer more memory penalties than non-numerical ones, for the latest ones, a very simple profiling analysis results in a performance very close to a conventional cache, in spite of its lower capacity.
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based detection of microsatellite instabilities in coding DNA sequences: a novel approach to identify DNA-mismatch repair-deficient cancer cells.

BACKGROUND Inherited defects in the DNA mismatch repair system lead to increased loss or gain of repeat units in microsatellites, commonly referred to as microsatellite instability (MSI). MSIs in coding regions of critical genes contribute to the pathogenesis of DNA-mismatch repair-deficient cancers, particularly those associated with the hereditary nonpolyposis colorectal cancer syndrome (HNPCC). MSI typing is therefore increasingly used to guide the molecular diagnosis of HNPCC. METHODS We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to identify MSIs in mononucleotide repeats within the coding sequences of genes relevant to the pathogenesis of MSI+ neoplastic lesions. After a primer extension reaction of PCR products encompassing the microsatellites, the molecular masses of the extension products were determined by MALDI-TOF-MS. RESULTS MSIs were detected by MALDI-TOF-MS in the GART, AC1, TGFBR2, MSH3, and MSH6 genes in neoplastic tissues and MSI+ colorectal cancer cell lines but not in MSI- control tissues. The analysis of peak-integral ratios in a single spectrum of the peaks representing insertions or deletions compared with the full-length microsatellites allowed relative quantification of MSIs. MALDI-TOF-MS-based genotyping results were confirmed by conventional DNA sequencing and electrophoresis. CONCLUSIONS Because of its reliability, short run times, and low costs, this semiquantitative procedure represents an effective alternative, in particular for diagnostic high-throughput typing of MSIs in neoplastic lesions.
Temporal specialization

The authors explore a variety of temporal relations with specialized relationships between transaction and valid time. An example is a retroactive temporal event relation, where the event must have occurred before it was stored, i.e., the valid time-stamp is restricted to be less than the transaction time-stamp. The authors discuss many useful restrictions, defining a large number of specialized types of temporal relations, and indicate some of their applications. A detailed taxonomy of specialized temporal relations is presented. This taxonomy may be used during database design to specify the particular time semantics of temporal relations. <<ETX>>
Mendelian randomization: Using genes as instruments for making causal inferences in epidemiology

Observational epidemiological studies suffer from many potential biases, from confounding and from reverse causation, and this limits their ability to robustly identify causal associations. Several high‐profile situations exist in which randomized controlled trials of precisely the same intervention that has been examined in observational studies have produced markedly different findings. In other observational sciences, the use of instrumental variable (IV) approaches has been one approach to strengthening causal inferences in non‐experimental situations. The use of germline genetic variants that proxy for environmentally modifiable exposures as instruments for these exposures is one form of IV analysis that can be implemented within observational epidemiological studies. The method has been referred to as ‘Mendelian randomization’, and can be considered as analogous to randomized controlled trials. This paper outlines Mendelian randomization, draws parallels with IV methods, provides examples of implementation of the approach and discusses limitations of the approach and some methods for dealing with these. Copyright © 2007 John Wiley & Sons, Ltd.
Effects of Early or Overexpression of the Autographa californica Multiple Nucleopolyhedrovirus orf94 (ODV-e25) on Virus Replication

odv-e25(e25) is one of the core genes of baculoviruses. To investigate how it functions in the replication cycle of a baculovirus, a number of Autographa californica multiple nucleopolyhedrovirus recombinants with e25 under control of the promoter of immediate early gene ie1, or the promoter of the very late hyperexpressed gene p10, were constructed using a bacmid system, and the effects of early expression or overexpression of e25 on replication of the virus were evaluated. Microscopy and titration assays demonstrated that bacmids with e25 under control of ie1 promoter were unable to produce budded viruses; and that the recombinant viruses with e25 under control of p10 promoter generated budded virus normally, but formation of occlusion bodies were dramatically reduced and delayed in the infected cells. Electron microscopy showed that there were no mature virions or intact nucleocapsids present in the cells transfected with a recombinant bacmid with e25 under control of ie1 promoter. Quantitative real-time PCR analysis demonstrated that alteration of the e25 promoter did not affect viral DNA synthesis. The reporter gene expression from the promoter of the major capsid protein gene vp39 was reduced 63% by early expression of e25. Confocal microscopy revealed that E25 was predominantly localized in nuclei by 24 hours post infection with wild-type virus, but it remained in the cytoplasm in the cells transfected with a recombinant bacmid with e25 under control of the ie1 promoter, suggesting that the transport of E25 into nuclei was regulated in a specific and strict time dependent manner.
A wavelet-based watermarking for digital images and video

Digital contents are copied easily because of the development of digital technology. So a digital watermark technique which aims at copyright protection of digital contents becomes more and more important, and various watermarking methods have been proposed. We proposed a method of digital watermark for still images by using wavelet packets, and examine the robustness of the watermarking method against several image processing. This method can be easily applied to the watermark for video because in this method, embedded data are detected without the original image. Therefore, we extend the wavelet-based watermarking method to the case of a watermark for video.
Dealing with heterogeneous big data when geoparsing historical corpora

It has long been known that `variety' is one of the key challenges and opportunities of big data. This is especially true when we consider the variety of content in historical corpora resulting from large-scale digitisation activities. Collections such as Early English Books Online (EEBO) and the British Library 19th Century Newspapers are extremely large and heterogeneous data sources containing a variety of content in terms of time, location, topic, style and quality. The range of geographical locations referenced in these corpora poses a difficult challenge for state of the art geoparsing tools. In the context of our work on Spatial Humanities analyses, we present our solution for dealing with the variety and scale of these corpora.
The Effect of the Real Exchange Rate on Technological Progress. An Application to the Textile Industry in China

Technological progress in the textile and clothing sectors is measured for 26 Chinese provinces using panel data by sector and the stochastic frontier method. The impact of the real exchange rate on this technological progress, as well as its transmission channels, are respectively estimated. The technological progress is positive for both sectors, and the real depreciation of the Chinese currency contributes to this improvement. Due to the dominant non state-owned enterprises in the clothing sector, both technological progress and the effect of real depreciation on the increase of technological progress are twice as high as in the textile sector. The principal transmission channel of the impact of the exchange rate on technological progress is through imported equipment, but not through openness.
Improved performance of large stroke comb-drive actuators by using a stepped finger shape

In this work we describe an electrostatic mass-balanced planar x/y-scanner, using an optimized comb finger shape, designed for parallel-probe storage applications. We show a new stepped comb finger shape design, that has superior force/displacement characteristics leading to a larger stroke at the same voltage and a larger available force compared to straight or tapered shapes.
Targeting mitotic chromosomes: a conserved mechanism to ensure viral genome persistence

Viruses that maintain their genomes as extrachromosomal circular DNA molecules and establish infection in actively dividing cells must ensure retention of their genomes within the nuclear envelope in order to prevent genome loss. The loss of nuclear membrane integrity during mitosis dictates that paired host cell chromosomes are captured and organized by the mitotic spindle apparatus before segregation to daughter cells. This prevents inaccurate chromosomal segregation and loss of genetic material. A similar mechanism may also exist for the nuclear retention of extrachromosomal viral genomes or episomes during mitosis, particularly for genomes maintained at a low copy number in latent infections. It has been heavily debated whether such a mechanism exists and to what extent this mechanism is conserved among diverse viruses. Research over the last two decades has provided a wealth of information regarding the mechanisms by which specific tumour viruses evade mitotic and DNA damage checkpoints. Here, we discuss the similarities and differences in how specific viruses tether episomal genomes to host cell chromosomes during mitosis to ensure long-term persistence.
Acoustic vector-sensor beamforming in the presence of flow noise

Passive sonar arrays are often used to find submerged vessels by measuring their radiated signal. Acoustic vector-sensor (AVS) arrays, which are normally towed by the ship at the ends of long cables, have been proven to be very effective for target direction of arrival (DOA) estimation. The flow noise, arising from the flow of water over the vector-sensor or its housing when the array is towed, is often a major source of interference to the towed array as it is usually directly coupled to the array sensing elements. In this paper, we obtain a closed-form expression for the spatial correlations of all the components of an AVS array in a flow-noise field. We apply the noise correlation model to DOA estimation using a uniform linear AVS array beamforming. The flow-noise impact on the beamforming capabilities is evaluated via numerical simulations.
Predicting the Mosquito Species and Vertebrate Species Involved in the Theoretical Transmission of Rift Valley Fever Virus in the United States

Rift Valley fever virus (RVFV) is a mosquito-borne virus in the family Bunyaviridiae that has spread throughout continental Africa to Madagascar and the Arabian Peninsula. The establishment of RVFV in North America would have serious consequences for human and animal health in addition to a significant economic impact on the livestock industry. Published and unpublished data on RVFV vector competence, vertebrate host competence, and mosquito feeding patterns from the United States were combined to quantitatively implicate mosquito vectors and vertebrate hosts that may be important to RVFV transmission in the United States. A viremia-vector competence relationship based on published mosquito transmission studies was used to calculate a vertebrate host competence index which was then combined with mosquito blood feeding patterns to approximate the vector and vertebrate amplification fraction, defined as the relative contribution of the mosquito or vertebrate host to pathogen transmission. Results implicate several Aedes spp. mosquitoes and vertebrates in the order Artiodactyla as important hosts for RVFV transmission in the U.S. Moreover, this study identifies critical gaps in knowledge which would be necessary to complete a comprehensive analysis identifying the different contributions of mosquitoes and vertebrates to potential RVFV transmission in the U.S. Future research should focus on (1) the dose-dependent relationship between viremic exposure and the subsequent infectiousness of key mosquito species, (2) evaluation of vertebrate host competence for RVFV among North American mammal species, with particular emphasis on the order Artiodactyla, and (3) identification of areas with a high risk for RVFV introduction so data on local vector and host populations can help generate geographically appropriate amplification fraction estimates.