Structured and Unstructured Information Extraction Using Text Mining and Natural Language Processing Techniques

Information on web is increasing at infinitum. Thus, web has become an unstructured global area where information even if available, cannot be directly used for desired applications. One is often faced with an information overload and demands for some automated help. Information extraction (IE) is the task of automatically extracting structured information from unstructured and/or semi-structured machine-readable documents by means of Text Mining and Natural Language Processing (NLP) techniques. Extracted structured information can be used for variety of enterprise or personal level task of varying complexity. The Information Extraction (IE) in also a set of knowledge in order to answer to user consultations using natural language. The system is based on a Fuzzy Logic engine, which takes advantage of its flexibility for managing sets of accumulated knowledge. These sets may be built in hierarchic levels by a tree structure. Information extraction is structured data or knowledge from unstructured text by identifying references to named entities as well as stated relationships between such entities. Data mining research assumes that the information to be “mined” is already in the form of a relational database. IE can serve an important technology for text mining. The knowledge discovered is expressed directly in the documents to be mined, then IE alone can serve as an effective approach to text mining. However, if the documents contain concrete data in unstructured form rather than abstract knowledge, it may be useful to first use IE to transform the unstructured data in the document corpus into a structured database, and then use traditional data mining tools to identify abstract patterns in this extracted data. We propose a novel method for text mining with natural language processing techniques to extract the information from data base with efficient way, where the extraction time and accuracy is measured and plotted with simulation. Where the attributes of entities and relationship entities from structured and semi structured information .Results are compared with conventional methods

TDMA- MAC Protocol based Energy- Potency for Periodic Sensing Applications in Wireless sensing Networks

Energy potency could be a major demand in wireless sensing element networks. Media Access management is one in every of the key areas wherever energy potency is achieved by planning such MAC protocol that's tuned to the necessities of the sensing element networks. Applications have different necessities and one MAC protocol can't be best TDMA-based MAC (TDMAC) protocol that is specially designed for such applications that need periodic sensing of the sensing element field. TDMAC organizes nodes into clusters. Nodes send their knowledge to their cluster head (CH) and CHs forward it to the bottom station. CHs removed from the bottom station use multi-hop communication by forwarding their knowledge to CHs nearer than themselves to the bottom station each put down-cluster and intra-cluster communication is only TDMA-based that effectively eliminates each inter cluster further as intra-cluster interference

Utilization of steel slag in development of sustainable and durable concrete.

This paper reflects the results of an experimental investigation of the strength, permeability, abrasion, carbonation, and shrinkage characteristics of concrete containing various percentages of steel slag as partial replacement of natural fine aggregates. M 30 Grade concrete was designed as per specific national specifications. Steel slag was used to replace natural sand in the range of 0– 50%. It was observed that the steel slag blended concrete with up to 50% substitution exhibited a comparable compressive and flexural strength when compared to the control specimens. From the Dorry’s abrasion test, it was noted that the specimens could be implemented in heavy-duty floor tiles and even extended to pavement construction. The shrinkage strains, water permeability, and carbonation of steel slag blended concrete were observed to be increasing with increasing replacement amounts of steel slag in the place of natural fine aggregates. The concrete containing steel slag replacing up to 40% of natural fine aggregates can be recommended for all heavy load involving structural applications, and substitution levels beyond 40% could be recommended for non-structural applications, pavements, etc

Safe and complete contig assembly via omnitigs

Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from $G$ as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201

Effects of intra-abdominal sepsis on atherosclerosis in mice

Introduction: Sepsis and other infections are associated with late cardiovascular events. Although persistent inflammation is implicated, a causal relationship has not been established. We tested whether sepsis causes vascular inflammation and accelerates atherosclerosis.Methods: We performed prospective, randomized animal studies at a university research laboratory involving adult male ApoE-deficient (ApoE-/-) and young C57B/L6 wild-type (WT) mice. In the primary study conducted to determine whether sepsis accelerates atherosclerosis, we fed ApoE-/- mice (N = 46) an atherogenic diet for 4 months and then performed cecal ligation and puncture (CLP), followed by antibiotic therapy and fluid resuscitation or a sham operation. We followed mice for up to an additional 5 months and assessed atheroma in the descending aorta and root of the aorta. We also exposed 32 young WT mice to CLP or sham operation and followed them for 5 days to determine the effects of sepsis on vascular inflammation.Results: ApoE-/- mice that underwent CLP had reduced activity during the first 14 days (38% reduction compared to sham; P < 0.001) and sustained weight loss compared to the sham-operated mice (-6% versus +9% change in weight after CLP or sham surgery to 5 months; P < 0.001). Despite their weight loss, CLP mice had increased atheroma (46% by 3 months and 41% increase in aortic surface area by 5 months; P = 0.03 and P = 0.004, respectively) with increased macrophage infiltration into atheroma as assessed by immunofluorescence microscopy (0.52 relative fluorescence units (rfu) versus 0.97 rfu; P = 0.04). At 5 months, peritoneal cultures were negative; however, CLP mice had elevated serum levels of interleukin 6 (IL-6) and IL-10 (each at P < 0.05). WT mice that underwent CLP had increased expression of intercellular adhesion molecule 1 in the aortic lumen versus sham at 24 hours (P = 0.01) that persisted at 120 hours (P = 0.006). Inflammatory and adhesion genes (tumor necrosis factor α, chemokine (C-C motif) ligand 2 and vascular cell adhesion molecule 1) and the adhesion assay, a functional measure of endothelial activation, were elevated at 72 hours and 120 hours in mice that underwent CLP versus sham-operations (all at P <0.05).Conclusions: Using a combination of existing murine models for atherosclerosis and sepsis, we found that CLP, a model of intra-abdominal sepsis, accelerates atheroma development. Accelerated atheroma burden was associated with prolonged systemic, endothelial and intimal inflammation and was not explained by ongoing infection. These findings support observations in humans and demonstrate the feasibility of a long-term follow-up murine model of sepsis

A pilot study for channel catfish whole genome sequencing and de novo assembly

<p>Abstract</p> <p>Background</p> <p>Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs. However, the average read lengths in next-generation sequencing technologies are short as compared with that of traditional Sanger sequencing. The short sequence reads pose great challenges for <it>de novo </it>sequence assembly. As a pilot project for whole genome sequencing of the catfish genome, here we attempt to determine the proper sequence coverage, the proper software for assembly, and various parameters used for the assembly of a BAC physical map contig spanning approximately a million of base pairs.</p> <p>Results</p> <p>A combination of low sequence coverage of 454 and Illumina sequencing appeared to provide effective assembly as reflected by a high N50 value. Using 454 sequencing alone, a sequencing depth of 18 X was sufficient to obtain the good quality assembly, whereas a 70 X Illumina appeared to be sufficient for a good quality assembly. Additional sequencing coverage after 18 X of 454 or after 70 X of Illumina sequencing does not provide significant improvement of the assembly. Considering the cost of sequencing, a 2 X 454 sequencing, when coupled to 70 X Illumina sequencing, provided an assembly of reasonably good quality. With several software tested, Newbler with a seed length of 16 and ABySS with a K-value of 60 appear to be appropriate for the assembly of 454 reads alone and Illumina paired-end reads alone, respectively. Using both 454 and Illumina paired-end reads, a hybrid assembly strategy using Newbler for initial 454 sequence assembly, Velvet for initial Illumina sequence assembly, followed by a second step assembly using MIRA provided the best assembly of the physical map contig, resulting in 193 contigs with a N50 value of 13,123 bp.</p> <p>Conclusions</p> <p>A hybrid sequencing strategy using low sequencing depth of 454 and high sequencing depth of Illumina provided the good quality assembly with high N50 value and relatively low cost. A combination of Newbler, Velvet, and MIRA can be used to assemble the 454 sequence reads and the Illumina reads effectively. The assembled sequence can serve as a resource for comparative genome analysis. Additional long reads using the third generation sequencing platforms are needed to sequence through repetitive genome regions that should further enhance the sequence assembly.</p

DNA Methylation in the Human Cerebral Cortex Is Dynamically Regulated throughout the Life Span and Involves Differentiated Neurons

The role of DNA cytosine methylation, an epigenetic regulator of chromatin structure and function, during normal and pathological brain development and aging remains unclear. Here, we examined by MethyLight PCR the DNA methylation status at 50 loci, encompassing primarily 5′ CpG islands of genes related to CNS growth and development, in temporal neocortex of 125 subjects ranging in age from 17 weeks of gestation to 104 years old. Two psychiatric disease cohorts—defined by chronic neurodegeneration (Alzheimer's) or lack thereof (schizophrenia)—were included. A robust and progressive rise in DNA methylation levels across the lifespan was observed for 8/50 loci (GABRA2, GAD1, HOXA1, NEUROD1, NEUROD2, PGR, STK11, SYK) typically in conjunction with declining levels of the corresponding mRNAs. Another 16 loci were defined by a sharp rise in DNA methylation levels within the first few months or years after birth. Disease-associated changes were limited to 2/50 loci in the Alzheimer's cohort, which appeared to reflect an acceleration of the age-related change in normal brain. Additionally, methylation studies on sorted nuclei provided evidence for bidirectional methylation events in cortical neurons during the transition from childhood to advanced age, as reflected by significant increases at 3, and a decrease at 1 of 10 loci. Furthermore, the DNMT3a de novo DNA methyl-transferase was expressed across all ages, including a subset of neurons residing in layers III and V of the mature cortex. Therefore, DNA methylation is dynamically regulated in the human cerebral cortex throughout the lifespan, involves differentiated neurons, and affects a substantial portion of genes predominantly by an age-related increase

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them