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.

LSB Matching Steganalysis Based on Patterns of Pixel Differences and Random Embedding

Peer-reviewed

Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences

Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (~800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.

Dynamic patterns of flow in the workplace: characterizing within-individual variability using a complexity science approach

As a result of the growing interest in studying employee well-being as a complex process that portrays high levels of within-individual variability and evolves over time, this present study considers the experience of flow in the workplace from a nonlinear dynamical systems approach. Our goal is to offer new ways to move the study of employee well-being beyond linear approaches. With nonlinear dynamical systems theory as the backdrop, we conducted a longitudinal study using the experience sampling method and qualitative semi-structured interviews for data collection; 6981 registers of data were collected from a sample of 60 employees. The obtained time series were analyzed using various techniques derived from the nonlinear dynamical systems theory (i.e., recurrence analysis and surrogate data) and multiple correspondence analyses. The results revealed the following: 1) flow in the workplace presents a high degree of within-individual variability; this variability is characterized as chaotic for most of the cases (75%); 2) high levels of flow are associated with chaos; and 3) different dimensions of the flow experience (e.g., merging of action and awareness) as well as individual (e.g., age) and job characteristics (e.g., job tenure) are associated with the emergence of different dynamic patterns (chaotic, linear and random).

Zonation patterns of benthic communities in an upwelling area from de western Mediterranean (La Herradura, Alboran Sea)

Species composition and distribution of marine benthic communities from La Herradura (Alboran Sea, western Mediterranean) are described to characterise its rocky and sedimentary bottoms bionomically. Rocky bottoms were studied by means of several underwater transects and soft bottoms with fixed stations along a bathymetric gradient. The study of the floristic and faunistic composition of the rocky benthic communities highlights depth as the main axis of variation. Factorial Correspondence Analysis segregates deep-water communities below 25 m depth (circalittoral communities) from shallower communities (axis I), and communities thriving between 5 and 25 m depth (lower infralittoral communities) from communities thriving close to the surface (shallow infralittoral communities) (axis II). The study of the sedimentary bottoms also suggests that depth, together with physical sedimentary properties, is the main axis of variation in species distribution. Floristic and faunistic records show the particular composition of La Herradura benthic communities, compared to Mediterranean and Atlantic ones. Mixing of Mediterranean and Atlantic waters, together with deep water upwelling episodes typical of this area, probably determine the peculiar composition of the benthic communities

Distribution Patterns of Soil Properties in a Rural Mediterranean Area in Northeastern Spain

Soil properties on the Cap de Creus Peninsula, NE Spain depend primarily on scarce agricultural practices and early abandonment. In the study area, 90% of which is mainly covered by Cistus shrubs, 8 environments representing variations in land use/land cover and soil properties at different depths were identified. In each environment variously vegetated areas were selected and sampled. The soils, collected at different depths, were classified as Lithic Xerorthents according to the United States Department of Agriculture system of soil classification (USDA-NRCS 1975). Differences in soil properties were largely found according to the evolution of the plant canopy and the land use history. To identify underlying patterns in soil properties related to environmental evolution, factor analysis was performed and factor scores were used to determine how the factor patterns varied between soil variables, soil depths and selected environments. The three-factor model always accounted for 80% of the total variation in the data at the different soil depths. Organic matter was the more relevant soil property at 0–2 cm depth, whereas active minerals (silt and clay) were found to be the most relevant soil parameters controlling soil dynamics at the other depths investigated. Results showed that vineyards and olive tree soils are poorly developed and present worse conditions for mineral and organic compounds. Analysis of factor scores allowed independent assessment of soils, depth and plant cover and demonstrated that soils present the best physico-chemical characteristics under Erica arborea and meadows. In contrast, soils under Cistus monspeliensis were less nutrient rich and less well structured

Patterns of impact resulting from a 'sit less, move more' web-based program in sedentary office employees

Purpose Encouraging office workers to ‘sit less and move more’ encompasses two public health priorities. However, there is little evidence on the effectiveness of workplace interventions for reducing sitting, even less about the longer term effects of such interventions and still less on dual-focused interventions. This study assessed the short and mid-term impacts of a workplace web-based intervention (Walk@WorkSpain, W@WS; 2010-11) on self-reported sitting time, step counts and physical risk factors (waist circumference, BMI, blood pressure) for chronic disease. Methods Employees at six Spanish university campuses (n=264; 42±10 years; 171 female) were randomly assigned by worksite and campus to an Intervention (used W@WS; n=129; 87 female) or a Comparison group (maintained normal behavior; n=135; 84 female). This phased, 19-week program aimed to decrease occupational sitting time through increased incidental movement and short walks. A linear mixed model assessed changes in outcome measures between the baseline, ramping (8 weeks), maintenance (11 weeks) and followup (two months) phases for Intervention versus Comparison groups.A significant 2 (group) × 2 (program phases) interaction was found for self-reported occupational sitting (F[3]=7.97, p=0.046), daily step counts (F[3]=15.68, p=0.0013) and waist circumference (F[3]=11.67, p=0.0086). The Intervention group decreased minutes of daily occupational sitting while also increasing step counts from baseline (446±126; 8,862±2,475) through ramping (+425±120; 9,345±2,435), maintenance (+422±123; 9,638±3,131) and follow-up (+414±129; 9,786±3,205). In the Comparison group, compared to baseline (404±106), sitting time remained unchanged through ramping and maintenance, but decreased at follow-up (-388±120), while step counts diminished across all phases. The Intervention group significantly reduced waist circumference by 2.1cms from baseline to follow-up while the Comparison group reduced waist circumference by 1.3cms over the same period. Conclusions W@WSis a feasible and effective evidence-based intervention that can be successfully deployed with sedentary employees to elicit sustained changes on “sitting less and moving more”.

Market entry patterns of Finnish SMEs entering China

In 2011 China became the world’s second largest economy overtaking Japan. With its rapidly growing middle class buying diverse goods from consumption products to sophisticated technology and luxury products, it is also the fastest growing export market in the world. The purpose of this study is to examine what types of market entry modes Finnish SMEs use in China, which factors affect on their decisions and whether they have switched or combined the strategies after entering China. The goal is to understand the relevance of the entry mode choice related to the internationalization process and to evaluate how well it suits the Chinese business environment. The empirical part of the study is a semi structured qualitative analysis of six case companies that represent different industry fields. The cases were selected based on the recent literature about the Finnish industry fields China is interested in to gain knowledge and expertise from. Companies included in the study are an architect office, two pharmaceutical development companies, an ICT company, a plastic mechanics company and a clean tech company. The results of this study indicated that the market entry patterns of Finnish SMEs in China differ from each other based on the factors related to company’s background, mode concerns and Chinese market influences.

Political participation beyond the vote : how the institutional context shapes patterns of political participation in 18 Western European democracies

Politiskt deltagande är en definierande del av varje demokratiskt politiskt system, även mellan valen. Men det har skett en betydande utveckling i vilka aktiviteter som uppfattas som politiskt deltagande. Det är inte enbart aktiviteter i politiska partier som är i fokus, men också olika protestaktiviteter, delaktighet i nya sociala rörelser och livsstilspolitik i form av politisk konsumtion. Politiskt deltagande mellan valen kan leda till en potentiell legitimitetskonflikt. Den potentiella konflikten mellan ansvarsutkrävande och medborgarnas aktiva medverkan har varit känd sedan länge. Representativa demokratier har genom olika institutionella mekanismer försökt konstruera ett fungerande politiskt system som förenar möjligheten för politiskt deltagande med en tydlig ansvarsstruktur. I detta sammanhang har den institutionella öppenheten haft en central position eftersom denna antas påverka hur lätt det är för medborgarna att påverka de formella beslutfattarna. Avhandlingen undersöker därmed konsekvenserna av institutionell öppenhet för olika former av politiskt deltagande. Resultaten tyder på att demokratiska staters institutionella uppbyggnad har väsentliga konsekvenser för det politiska deltagandet. Men samspelet mellan systemet och deltagandet verkar vara mera invecklat än de dominerande teorierna om politiska institutioner och deltagande ger vid handen. Institutionell öppenhet har inte den förväntade effekt beroende på om den politiska handlingen sker inom eller utanför det formella systemet, och den institutionella effekten är mera uttalad för föreningsaktivism och politisk konsumtion, vilket är de aktiviteter som ligger längst bort från det formella politiska systemet. Resultaten utmanar därmed centrala teoretiska antaganden inom forskningen om politiskt deltagande. I ljuset av de resultat som presenteras i avhandlingen framstår det som särskilt angeläget att omvärdera effekten av institutionell öppenhet.

Effects of global climate changes on geographical distribution patterns of economically important plant species in cerrado

Different climate models, modeling methods and carbon emission scenarios were used in this paper to evaluate the effects of future climate changes on geographical distribution of species of economic and cultural importance across the Cerrado biome. As the results of several studies have shown, there are still many uncertainties associated with these projections, although bioclimatic models are still widely used and effective method to evaluate the consequences for biodiversity of these climate changes. In this article, it was found that 90% of these uncertainties are related to methods of modeling, although, regardless of the uncertainties, the results revealed that the studied species will reduce about 78% of their geographic distribution in Cerrado. For an effective work on the conservation of these species, many studies still need to be carried out, although it is already possible to observe that climate change will have a strong influence on the pattern of distribution of these species.

Patterns of parasitism by Amblyomma rotundatum (Ixodidae) on Rhinella schneideri (Bufonidae) in islands of São Francisco River, Minas Gerais, Brazil

Abstract: We sampled ticks from specimens of the rococo toad Rhinella schneideriby flannel dragging on two Islands located in the São Francisco River near the Três Marias hydroelectric dam, southeastern Brazil. A total of 120 toads was examined, of which 63 (52.5%) were parasitized only by Amblyomma rotundatumtotaling 96 larvae, 163 nymphs and 134 females. The burden of parasitism ranged from one to 43 ticks, with a mean intensity of infestation of 6.2±5.5 ticks per host. The tick A. rotundatumexhibited highly aggregated distribution. Peak abundance of larvae and nymphs occurred in the dry season (May to September), whereas peak abundance of females occurred in the wet season (October to April). We collected most ticks near the head and hind limbs of R. schneideri. The finding of two engorged A. rotundatumnymphs in the same resting places of two toads and the absence of this species in the dragged areas suggest a nidicolous behavior at the studied site.

Supplier codes of conduct: Acting responsibly in global supply chains

Nowadays the Western companies are considered responsible for the social and environmental issues in their whole supply chains. To influence the practices of their suppliers the Western companies have created suppliers codes of conduct (SCCs) which express their requirements. Suppliers’ compliance with the SCCs is checked through audits. The purpose of this thesis is to analyze SCCs as a means for Western companies to ensure socially and environmentally responsible actions in their global supply chains, and the sub-objectives are to find out 1) how well do the SCCs and their auditing work at suppliers’ production sites and 2) how can possible problems related to SCCs and their auditing be solved. This is a qualitative research carried out in the form of a case study with two case companies. In this study both primary and secondary data is used. The primary data is collected in the form of interviews of the case company representatives and three external experts. Based on a theoretical framework of previous research in the fields of corporate social responsibility and supply chain management, a model with eleven factors, which influence the success of SCC implementation and the auditing of SCC –implementation, is drafted. Also several different best-practices to help to solve and avoid possible problems related to SCC -implementation and auditing have been identified from previous research. Based on the findings of this study the theoretical model has been updated adding two new influential factors. It seems that how well the SCC and its auditing work at suppliers’ production sites depends on the joint effect of thirteen influential factors: buyer’s purchasing policy, supplier’s motivation, buyer’s commitment, the solving of agency problems, the contents of the SCC, supplier’s role and the buyer-supplier –relationship, complexity of supply chain, the limitations of the smaller buyers, cooperation through a business association or multi-stakeholder system, the role of supplier’s employees, SCC –related communication and supplier’s understanding, cheating in audits and the auditors. The possible problems related to SCCs and their auditing can be solved by adopting best-practices. Nine of the theoretical best-practices stand out from the findings of this study: 1) two-way communication and collecting feedback from suppliers, 2) the philosophy of continuous improvement, 3) long-term business relationships with the supplier, 4) informing the supplier about the advantages of SCC –compliance, 5) rewarding code-compliant suppliers, 6) building collaborative, good buyer-supplier relationships, 7) supporting and advising the supplier, 8) joining a business association or multi-stakeholder system and 9) interviewing supplier’s employees as a part of the audits.

Patterns of spatial distribution in macroalgal communities from tropical lotic ecosystems

Three sampling sites were analysed in each of the following tropical regions: 1) northwestern São Paulo State, representing a disturbed region; 2) Bonito, Mato Grosso do Sul State, representing a hard water region; and 3) Ubatuba, northern costal region of São Paulo State, a well preserved tropical rainforest region. The hard water region had the highest mean values for macroalgal species richness (6.3) and diversity index (H' = 0.62). Northwest and rainforest regions had the highest percent cover values (22.5% and 17.0%, respectively). All sites in the northwest region had one or two dominant species (percent cover significantly higher than the remaining species), characterizing the niche pre-emption distribution pattern. The same pattern was found in two sites of the Atlantic rainforest. The hard water region had dominance of one species in two out of the three sites, but differently from the northwest region, niche overlap values were lower, evidencing a patch distribution. Competition for space was one of the main factors to explain spatial distribution. Overall, sites characterized by niche pre-emption had lower species richness, higher values for niche width and overlap, dominance index and percent cover of dominant species. In contrast, sites characterized by patch distribution had higher species richness and lower values for niche overlap and width, dominance index and percent cover.

Patterns of litter production in a secondary alluvial Atlantic Rain Forest in southern Brazil

Above-ground litter production is one of the most accessible ways to estimate ecosystem productivity, nutrient fluxes and carbon transfers. Phenological patterns and climatic conditions are still not fully explained well for tropical and subtropical forests under less pronounced dry season and non-seasonal climates, as well as the interaction of these patterns with successional dynamics. Monthly litterfall was estimated for two years in a 9 to 10 year old secondary alluvial Atlantic Rain forest. Total litterfall was higher in the site with more developed vegetation (6.4 ± 1.2 ton ha-1 year-1; 95% confidence interval) as compared to the site with less developed vegetation (3.0 ± 1.0 ton ha-1 year-1). The monthly production of 11 litter fractions (eight fractions comprising the leaf litter of the seven main species of the community and other species; reproductive parts, twigs £ 2 cm diameter, and miscellaneous material) were correlated with meteorological variables making possible to identify three patterns of deposition. The main pattern, dominated by leaf-exchanging species, consisted of a cycle with the highest litterfall at the beginning of the rainy season, preceding by basically three months the peaks of the annual cycles of rainfall and temperatures. Other two patterns, dominated by brevi-deciduous species, peaked at the end of the rainy season and at the end of the non-rainy season. Tropical and subtropical dry forests that present the highest leaf fall gradually earlier than rain forests (as the studied sites) are possibly related to the start of senescence process. It seems that such process is triggered earlier by a more severe hydric stress, besides other factors linked to a minor physiological activity of plants that result in abscission.

Effects of host resistance on the isozymatic patterns of Bipolaris sorokiniana (Dematiaceae, Moniliales)

Nine isolates of Bipolaris sorokiniana were inoculated on three cultivars of wheat plants (susceptible, moderately resistant, resistant). Eight days after the inoculation, the isolates were recovered (27 isolates) and the following isozymatic patterns were analyzed: esterase, alkaline phosphatase, acid phosphatase, malate dehydrogenase, and superoxide dismutase. The esterase system was the most polymorphic, and the isolates recovered from the susceptible cultivar showed the highest variability. This is evidence that this cultivar exerts low selection pressure on the pathogen