Stronger Lempel-Ziv Based Compressed Text Indexing

Given a text T[1..u] over an alphabet of size σ, the full-text search problem consists in finding the occ occurrences of a given pattern P[1..m] in T. In indexed text searching we build an index on T to improve the search time, yet increasing the space requirement. The current trend in indexed text searching is that of compressed full-text self-indices, which replace the text with a more space-efficient representation of it, at the same time providing indexed access to the text. Thus, we can provide efficient access within compressed space. The Lempel-Ziv index (LZ-index) of Navarro is a compressed full-text self-index able to represent T using 4uH _k (T)+o(ulog?σ) bits of space, where H _k (T) denotes the k-th order empirical entropy of T, for any k=o(log? _σ u). This space is about four times the compressed text size. The index can locate all the occ occurrences of a pattern P in T in O(m ³log?σ+(m+occ)log?u) worst-case time. Although this index has proven very competitive in practice, the O(m ³log?σ) term can be excessive for long patterns. Also, the factor 4 in its space complexity makes it larger than other state-of-the-art alternatives. In this paper we present stronger Lempel-Ziv based indices (LZ-indices), improving the overall performance of the original LZ-index. We achieve indices requiring (2+ε)uH _k (T)+o(ulog?σ) bits of space, for any constant ε>0, which makes them the smallest existing LZ-indices. We simultaneously improve the search time to O(m ²+(m+occ)log?u), which makes our indices very competitive with state-of-the-art alternatives. Our indices support displaying any text substring of length ? in optimal O(?/log? _σ u) time. In addition, we show how the space can be squeezed to (1+ε)uH _k (T)+o(ulog?σ) to obtain a structure with O(m ²) average search time for m≥2log? _σ u. Alternatively, the search time of LZ-indices can be improved to O((m+occ)log?u) with (3+ε)uH _k (T)+o(ulog?σ) bits of space, which is much less than the space needed by other Lempel-Ziv-based indices achieving the same search time. Overall our indices stand out as a very attractive alternative for space-efficient indexed text searching.     

Composite indicator for railway infrastructure management

Railway Engineering Science - The assessment and analysis of railway infrastructure capacity is an essential task in railway infrastructure management carried out to meet the required quality and...     

Dynamic deformation behavior of ultrafine-grained low-carbon steels fabricated by equal-channel angular pressing

The dynamic deformation behavior of ultrafine-grained low-carbon steels fabricated by equal-channel angular pressing (ECAP) was investigated in this study. Dynamic torsional tests, using a torsional Kolsky bar, were conducted on four steel specimens, two of which were annealed at 480 °C after ECAP, and then the test data were compared in terms of microstructures, tensile properties, and adiabatic shear-band formation. The equal-channel angular pressed specimen consisted of very fine, equiaxed grains of 0.2 to 0.3 μm in size, which were slightly coarsened after annealing. The dynamic torsional test results indicated that maximum shear stress decreased with increasing annealing time, whereas fracture shear strain increased. Some adiabatic shear bands were observed at the gage center of the dynamically deformed torsional specimen. Their width was smaller in the equal-channel angular pressed specimen than in the 1-hour-annealed specimen, but they were not found in the 24-hour-annealed specimen. Ultrafine, equiaxed grains of 0.05 to 0.2 μm in size were formed inside the adiabatic shear band, and their boundaries had characteristics of high-angle grain boundaries. These phenomena were explained by dynamic recrystallization due to a highly localized plastic strain and temperature rise during dynamic deformation.     

Fine structure of the male accessory glands of Triatoma rubrofasciata (De Geer, 1773) (Hemiptera, Triatominae)

Male of Triatoma rubrofasciata has four elongated sac-like reproductive mesodermic accessory glands, lined by an inner single layer of secretory cells, with basal plasma membrane infolds and short apical microvilli, and externally enveloped by a thin visceral muscle layer. The secretory cells have a well-developed rough endoplasmic reticulum, Golgi complex, mitochondria, and secretory granules. In one day old adult the gland cells are poorly developed, presenting small, electron-transparent secretory granules scattered among the rough endoplasmatic reticulum, whereas in three days old adult these cells have the cisternae of the rough endoplasmatic reticulum varing size degree, filled with granular electrondense content. In five days old males the secretory granules increase in diameter, being released to the gland lumen. Therefore, there is an increase of the secretory activity according to male maturation.     

An E3‐14.7K Peptide that Promotes Microtubules‐Mediated Transport of Plasmid DNA Increases Polyplexes Transfection Efficiency

Chemical vectors as cationic polymers and cationic lipids are promising alternatives to viral vectors for gene therapy. Beside endosome escape and nuclear import, plasmid DNA (pDNA) migration in the cytosol toward the nuclear envelope is also regarded as a limiting step for efficient DNA transfection with non‐viral vectors. Here, the interaction between E3‐14.7K and FIP‐1 to favor migration of pDNA along microtubules is exploited. E3‐14.7K is an early protein of human adenoviruses that interacts via FIP‐1 (Fourteen.7K Interacting Protein 1) protein with the light‐chain components of the human microtubule motor protein dynein (TCTEL1). This peptide is conjugated with pDNA and mediates interaction of pDNA in vitro with isolated microtubules as well as with microtubules in cellulo. Videomicroscopy and tracking treatment of images clearly demonstrate that P79‐98/pDNA conjugate exhibits a linear transport with large amplitude along microtubules upon 2 h transfection with polyplexes whereas control pDNA conjugate exhibits small non‐directional movements in the cytoplasm. Remarkably, P79‐98/peGFP polyplexes enhance by a factor 2.5 (up to 76%) the number of transfected cells. The results demonstrate, for the first time, that the transfection efficiency of polyplexes can be drastically increased when the microtubules migration of pDNA is facilitated by a peptide allowing pDNA docking to TCTEL1. This is a real breakthrough in the non viral gene delivery field that opens hope to build artificial viruses.     

LncRNA H19 Impairs Chemo and Radiotherapy in Tumorigenesis

Various treatments based on drug administration and radiotherapy have been devoted to preventing, palliating, and defeating cancer, showing high efficiency against the progression of this disease. Recently, in this process, malignant cells have been found which are capable of triggering specific molecular mechanisms against current treatments, with negative consequences in the prognosis of the disease. It is therefore fundamental to understand the underlying mechanisms, including the genes—and their signaling pathway regulators—involved in the process, in order to fight tumor cells. Long non-coding RNAs, H19 in particular, have been revealed as powerful protective factors in various types of cancer. However, they have also evidenced their oncogenic role in multiple carcinomas, enhancing tumor cell proliferation, migration, and invasion. In this review, we analyze the role of lncRNA H19 impairing chemo and radiotherapy in tumorigenesis, including breast cancer, lung adenocarcinoma, glioma, and colorectal carcinoma.     

Chronic-Antibiotics Induced Gut Microbiota Dysbiosis Rescues Memory Impairment and Reduces β-Amyloid Aggregation in a Preclinical Alzheimer’s Disease Model

Alzheimer’s disease (AD) is a multifactorial pathology characterized by β-amyloid (Aβ) deposits, Tau hyperphosphorylation, neuroinflammatory response, and cognitive deficit. Changes in the bacterial gut microbiota (BGM) have been reported as a possible etiological factor of AD. We assessed in offspring (F1) 3xTg, the effect of BGM dysbiosisdysbiosis in mothers (F0) at gestation and F1 from lactation up to the age of 5 months on Aβ and Tau levels in the hippocampus, as well as on spatial memory at the early symptomatic stage of AD. We found that BGM dysbiosisdysbiosis with antibiotics (Abx) treatment in F0 was vertically transferred to their F1 3xTg mice, as observed on postnatal day (PD) 30 and 150. On PD150, we observed a delay in spatial memory impairment and Aβ deposits, but not in Tau and pTau protein in the hippocampus at the early symptomatic stage of AD. These effects are correlated with relative abundance of bacteria and alpha diversity, and are specific to bacterial consortia. Our results suggest that this specific BGM could reduce neuroinflammatory responses related to cerebral amyloidosis and cognitive deficit and activate metabolic pathways associated with the biosynthesis of triggering or protective molecules for AD.     

Downstream environmental effects of dam operations: Changes in habitat quality for native fish species

Hydropeaking dam operation and water extractions for irrigation have been broadly stated as alterations to natural flow regimes, which have also been noticed in the Biobío Watershed, in Central Chile, since 1996. In the Biobío River, most of native fish species are endemic and very little is known about them. Their ecological and social values have never been estimated, and there is lack of information about their habitat preferences. Furthermore, changes on fish habitat availability due to natural and/or man‐made causes have not been evaluated. In this study, eight native fish species, in a representative reach of the Biobío River, were studied and their preferred habitats were surveyed and characterized. A hydrodynamic model was built and linked to the fish habitat simulation model CASiMiR. Fuzzy rules and fuzzy sets were developed for describing habitat preference of the native fish species. CASiMiR was then used to simulate how physical habitat conditions vary due to flow control (i.e. upstream dams). Results show how overall habitat quality, expressed as weighted usable area (WUA) and hydraulic habitat suitability (HHS), changes and fluctuates due to the dam operation and how the daily hydropeaking is influencing quantity, quality and location of different habitats. The study suggests that the analysed fish are highly susceptible to flow control, as dams are currently operated, and fish habitat improvement suggestions are proposed. Copyright © 2010 John Wiley & Sons, Ltd.     

A microfluidic approach for development of hybrid collagen-chitosan extracellular matrix-like membranes for on-chip cell cultures

To advance organ-on-a-chip development and other areas befitting from physiologically-relevant biomembranes,a microfluidic platform is presented for synthesis of biomembranes during gelation and investigation into their role as extracellular matrix supports.In this work,high-throughput studies of collagen,chitosan,and collagen-chitosan hybrid biomembranes were carried out to characterize and compare key properties as a function of the applied hydrodynamic conditions during gelation.Specifically,depending on the biopolymer material used,varying flow conditions during biomembrane gelation caused width,uniformity,and swelling ratio to be differently affected and controllable.Finally,cell viability studies of seeded fibroblasts were conducted,thus showing the potential for biological applications.     

Automatic bearing fault diagnosis based on one-class ν-SVM

Rolling-element bearings are among the most used elements in industrial machinery, thus an early detection of a defect in these components is necessary to avoid major machine failures. Vibration analysis is a widely used condition monitoring technique for high-speed rotating machinery. Using the information contained in the vibration signals, an automatic method for bearing fault detection and diagnosis is presented in this work. Initially, a one-class ν-SVM is used to discriminate between normal and faulty conditions. In order to build a model of normal operation regime, only data extracted under normal conditions is used. Band-pass filters and Hilbert Transform are then used sequentially to obtain the envelope spectrum of the original raw signal that will finally be used to identify the location of the problem. In order to check the performance of the method, two different data sets are used: (a) real data from a laboratory test-to-failure experiment and (b) data obtained from a fault-seeded bearing test. The results showed that the method was able not only to detect the failure in an incipient stage but also to identify the location of the defect and qualitatively assess its evolution over time.