Identification of molecular subtypes and gene expression patterns of breast cancer analysing RNA-seq data

Breast cancer is the most common diagnosed cancer and the leading cause of cancer death among females worldwide. It is considered a highly heterogeneous disease and it must be classified into more homogeneous groups. Hence, the purpose of this study was to classify breast tumors based on variations in gene expression patterns derived from RNA sequencing by using different class discovery methods. 42 breast tumors paired-samples were sequenced by Illumine Genome Analyzer and the data was analyzed and prepared by TopHat2 and htseq-count. As reported previously, breast cancer could be grouped into five main groups known as basal epithelial-like group, HER2 group, normal breast-like group and two Luminal groups with a distinctive expression profile. Classifying breast tumor samples by using PAM50 method, the most common subtype was Luminal B and was significantly associated with ESR1 and ERBB2 high expression. Luminal A subtype had ESR1 and SLC39A6 significant high expression, whereas HER2 subtype had a high expression of ERBB2 and CNNE1 genes and low luminal epithelial gene expression. Basal-like and normal-like subtypes were associated with low expression of ESR1, PgR and HER2, and had significant high expression of cytokeratins 5 and 17. Our results were similar compared with TGCA breast cancer data results and with known studies related with breast cancer classification. Classifying breast tumors could add significant prognostic and predictive information to standard parameters, and moreover, identify marker genes for each subtype to find a better therapy for patients with breast cancer.

Identification of metabolites and thermal transformation products of quinolones in raw cow milk by liquid chromatography coupled to high resolution mass spectrometry.

The presence of residues of antibiotics, metabolites, and thermal transformation products (TPs), produced during thermal treatment to eliminate pathogenic microorganisms in milk, could represent a risk for people. Cow"s milk samples spiked with enrofloxacin (ENR), ciprofloxacin (CIP), difloxacin (DIF), and sarafloxacin (SAR) and milk samples from cows medicated with ENR were submitted to several thermal treatments. The milk samples were analyzed by liquid chromatography-mass spectrometry (LC-MS) to find and identify TPs and metabolites. In this work, 27 TPs of 4 quinolones and 24 metabolites of ENR were found. Some of these compounds had been reported previously, but others were characterized for the first time, including lactose-conjugated CIP, the formamidation reaction for CIP and SAR, and hydroxylation or ketone formation to produce three different isomers for all quinolones studied.

Market Opportunities for Paper Industry in Radio Frequency Identification

The paper industry has been experiencing remarkable structural changes since paper demand growth has ceased and some markets are declining. One reason behind the declined demand is the Internet, which has partially substituted the newspaper as a source of information. Paper products alone can no longer provide livelihood, and the paper industry has to find new business areas. In this research, we studied radio frequency identification (RFID), and the market opportunities it could provide for paper industry. The research combined a quantitative industry analysis and qualitative interviews. RFID is a growing industry in the beginning of its life cycle, in which value chains and technologies still evolve significantly. The industry is going to concentrate on the future, and in the long term RFID-identifiers will probably be printed on paper substrate or directly onto products. Paper industry has the chance to enter the RFID industry, but it has to obtain the required competences, for example through acquisitions. The business potential RFID offers to paper industry is inadequate, and while reviewing new strategic options, the paper industry must consider more options, for example the entire printed intelligence.

Improving the Potentials of Logistics Processes: Identification and Solutions

The importance of logistics for companies is a well known and justified issue. Today, enterprises are developing their logistics processes in order to match their products and services to the requirements of the most important customers. Therefore there is a need for developing analysing tools for logistics and especially for analysing the significance of various customer service elements. The aim of this paper is to propose analytic tools for supporting strategic level logistics decision making by emphasizing service level elements on two levels: (1) to introduce and propose approaches to categorize the developing efforts of logistics and (2) to introduce and/or propose approaches for solving some customer service related strategic level logistics problems. This study consists of two parts. In the first part an overview of the work is presented, and the second part comprises eight research papers on the topic of the study. The overview includes an introduction, where strategic and tactical level logistics problems are discussed and the relation of logistics to marketing and customer service issues is presented. In the first part of the study the objectives, the structure, the research strategy and the contribution of the research are described, and the challenges for future research are discussed. In the second part the three first papers deal with the identification of objectives for logistics while the remaining five papaers concentrate on solving customer service related strategic level logistics problems.

Identification of paintings from camera-phone images

Peer-reviewed

Identification of Turning Points in the Research on Titanium Dioxide Production and Application

This dissertation "Identification of turning points in the research on titanium dioxide production and application" aims at detecting in scientific literatures emerging trends and sudden changes in titanium dioxide production and application. These key changes are then studied to determine its transient patterns and its effect on the research on titanium dioxide production and application The source of information is from bibliographic data which discussed titanium dioxide production and application. These bibliographic data where obtained from ISI Web of Knowledge and then formed into a network of clusters by applying software called Citespace.

Identification of acetates in elasmopalpulus lignosellus pheromone glands using a newly created mass spectral database and kóvats retention indices

Based on a specially created mass spectral database utilizing 23 tetradecenyl and 22 hexadecenyl acetate standards along with Kóvats retention indices obtained on a very polar stationary phase [poly (biscyanopropyl siloxane)] (SP 2340), (Z)-9-hexadecenyl acetate, (Z)-11-hexadecenyl acetate and (E)-8-hexadecenyl acetate were identified in active pheromone extracts of Elasmopalpus lignosellus. This identification was more efficient than our previous study using gas chromatography/mass spectrometry with a dimethyl disulfide derivative where we could only identify the first two acetates. The acetate composition of the pheromone gland differed from region to region in Brazil and from that from the Tifton (GA, USA) population, suggesting polymorphism or a different sub-species.

Identification of the Emerging Issues in Recycled Fiber Processing

The objectives of this research work “Identification of the Emerging Issues in Recycled Fiber processing” are discovering of emerging research issues and presenting of new approaches to identify promising research themes in recovered paper application and production. The projected approach consists of identifying technological problems often encountered in wastepaper preparation processes and also improving the quality of recovered paper and increasing its proportion in the composition of paper and board. The source of information for the problem retrieval is scientific publications in which waste paper application and production were discussed. The study has exploited several research methods to understand the changes related to utilization of recovered paper. The all assembled data was carefully studied and categorized by applying software called RefViz and CiteSpace. Suggestions were made on the various classes of these problems that need further investigation in order to propose an emerging research trends in recovered paper.

Garlic viral complex: identification of Potyviruses and Carlavirus in Central Brazil

Garlic viruses often occur in complex infections in nature. In this study, a garlic virus complex, collected in fields in Brazil, was purified. RT-PCR was performed using specific primers designed from the consensus regions of the coat protein genes of Onion yellow dwarf virus, a garlic strain (OYDV-G) and Leek yellow stripe virus (LYSV). cDNA of Garlic common latent virus (GCLV) was synthesized using oligo-dT and random primers. By these procedures individual garlic virus genomes were isolated and sequenced. The nucleotide sequence analysis associated with serological data reveals the presence of two Potyvirus OYDV-G and LYSV, and GCLV, a Carlavirus, simultaneously infecting garlic plants. Deduced amino acid sequences of the Brazilian isolates were compared with related viruses reported in different geographical regions of the world. The analysis showed closed relations considering the Brazilian isolates of OYDV-G and GCLV, and large divergence considering LYSV isolate. The detection of these virus species was confirmed by specific reactions observed when coat protein genes of the Brazilian isolates were used as probes in dot-blot and Southern blot hybridization assays. In field natural viral re-infection of virus-free garlic was evaluated.

Identification of Phaeoisariopsis griseola pathotypes from five States in Brazil

Due to the increased importance of angular leaf spot of common bean (Phaseolus vulgaris) in Brazil, monitoring the pathogenic variability of its causal agent (Phaeoisariopsis griseola) is the best strategy for a breeding program aimed at developing resistant genotypes. Fifty one isolates of P. griseola collected in five Brazilian States were tested on a set of 12 international differential cultivars in the greenhouse. When inoculated plants showed symptoms but no sporulation was observed, they were transferred to a moist chamber for approximately 20-24 h. After this period of time, if no sporulation was observed, the plants were considered resistant; otherwise, they were considered susceptible. From the fifty-one tested isolates, seven different pathotypes were identified. No Andean pathotypes were identified; consequently, all isolates were classified as Middle American pathotypes. Pathotype 63-31 was the most widespread. Pathotype 63-63 overcame resistance genes present in all differential cultivars and also the resistance gene(s) present in the cultivar AND 277. This fact has important implications for breeding angular leaf spot resistance in beans, and suggests that searching for new resistance genes to angular leaf spot must be pursued.

Identification of rapd marker linked to blast resistance gene in a somaclone of rice cultivar Araguaia

The gene Pi-ar confers resistance to Pyricularia grisea race IB-45 in a somaclone derived from immature panicles of the susceptible rice (Oryza sativa) cultivar Araguaia. RAPD technique was used to identify molecular markers linked to this gene utilizing bulked segregant analysis. Initially, the two parental DNAs from the resistant donor SC09 and 'Araguaia' were analyzed using random primers. Of the 240 primers tested, 203 produced amplification products. The two parental DNAs along with the resistant and susceptible bulks of F2 population were screened using 48 primers that differentiated resistant and susceptible parents. Even though eight primers differentiated the resistant bulk from the susceptible bulk, as well as somaclone SC09 and 'Araguaia', only one primer, OPC02 ('GTGAGGCGTC'), was found to be tightly linked (1.7cM) to the resistance gene of somaclone SC09.

Genetic linkage map of Phaseolus vulgaris and identification of QTLs responsible for resistance to Xanthomonas axonopodis pv. phaseoli

Common bean (Phaseolus vulgaris) cultivars with a high degree of resistance to Xanthomonas axonopodis pv. phaseoli (Xap) are not available in Brazil. Despite many studies, a low degree of resistance to Xap continues to exist due to its complex genetic inheritance, which is not well known. The objectives of this research were to complement a common bean genetic map based on the cross between a susceptible genotype 'HAB-52' and a resistant genotype 'BAC-6', and to map and analyze genomic regions (quantitative trait loci – QTLs) related to Xap resistance. Eleven linkage groups were determined using 143 RAPD markers, covering 1,234.5 cM of the genome. This map was used to detect QTLs associated with Xap resistance on leaves and pods. The averages of disease severity on leaves (represented by the transformed disease index – TDI) and pods (represented by the diameter of lesion on pods – DLP) were added to the data of the linkage map. Five TDI QTLs and only one LDP QTL were detected. The TDI QTLs were placed in the A, B, G and J linkage groups, with phenotypic variations ranging from 12.7 to 71.6%. The DLP QTL explained 12.9% of the phenotypic variation and was mapped in a distinct linkage group. These results indicate that there are different genes involved in the control of resistance on leaves and pods.

Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences

The aim of this study was to identify isolates of Rhizoctonia solani causing hypocotyl rot and foliar blight in soybean (Glycine max) in Brazil by the nucleotide sequences of ITS-5.8S regions of rDNA. The 5.8S rDNA gene sequence (155 bp) was highly conserved among all isolates but differences in length and nucleotide sequence of the ITS1 and ITS2 regions were observed between soybean isolates and AG testers. The similarity of the nucleotide sequence among AG-1 IA isolates, causing foliar blight, was 95.1-100% and 98.5-100% in the ITS1 and ITS2 regions, respectively. The nucleotide sequence similarity among subgroups IA, IB and IC ranged from 84.3 to 89% in ITS1 and from 93.3 to 95.6% in ITS2. Nucleotide sequence similarity of 99.1% and 99.3-100% for ITS1 and ITS2, respectively, was observed between AG-4 soybean isolates causing hypocotyl rots and the AG-4 HGI tester. The similarity of the nucleotide sequence of the ITS-5.8S rDNA region confirmed that the R. solani Brazilian isolates causing foliar blight are AG-1 IA and isolates causing hypocotyl rot symptoms are AG-4 HGI. The ITS-5.8S rDNA sequence was not determinant for the identification of the AG-2-2 IIIB R. solani soybean isolate.

Identification of the major fungitoxic component of cinnamon bark oil

The study was done to identify the most active fungitoxic component of cinnamon bark (Cinnamomum zeylanicum) oil that can be used as a marker for standardization of cinnamon extract or oil based natural preservative of stored seeds. Aspergillus flavus and A. ruber were used as test fungi. The hexane extracted crude oil and the hydro-distilled essential oil from cinnamon bark had complete growth inhibition concentration (CGIC) of 300 and 100 µl/l, respectively. Both oils produced three fractions on preparative thin layer silica-gel chromatography plates. The fraction-2 of either oil was the largest and most active, with CGIC of 200 µl/l, but the fungitoxicity was also retained in the other two fractions. The fraction-1 and 3 of the crude oil reduced growth of both the fungal species by 65%, and those of distilled oil by 45% at 200 µl/l. The CGIC of these fractions from both the sources was above 500 µl/l. The gas chromatography and mass spectrometry (GC-MS) of the fraction-2 of the hexane extract revealed that it contained 61% cinnamaldehyde, 29% cinnamic acid, and two minor unidentified compounds in the proportion of 4% and 6%. The GC-MS of the fraction-2 of the distilled oil revealed that it contained 99.1% cinnamaldehyde and 0.9% of an unidentified compound. The CGIC of synthetic cinnamaldehyde was 300 µl/l and that of cinnamic acid above 500 µl/l. The 1:1 mixture of cinnamaldehyde and cinnamic acid had CGIC of 500 µl/l. The data revealed that cinnamaldehyde was the major fungitoxic component of hexane extract and the distilled essential oil of cinnamon bark, while other components have additive or synergistic effects on total fungitoxicity. It is suggested that the natural seed preservative based on cinnamon oil can be standardized against cinnamaldehyde.