An in silico method for detecting overlapping functional modules from composite biological networks

<p>Abstract</p> <p>Background</p> <p>The ever-increasing flow of gene expression and protein-protein interaction (PPI) data has assisted in understanding the dynamics of the cell. The detection of functional modules is the first step in deciphering the apparent modularity of biological networks. However, most network-partitioning algorithms consider only the topological aspects and ignore the underlying functional relationships.</p> <p>Results</p> <p>In the current study we integrate proteomics and microarray data of yeast, in the form of a weighted PPI graph. We partition the enriched PPI network with the novel DetMod algorithm and we identify 335 modules. One of the main advantages of DetMod is that it manages to capture the inter-module cross-talk by allowing a controlled degree of overlap among the detected modules. The obtained modules are densely connected in terms of protein interactions, while their members share up to a high degree similar biological process GO terms.</p> <p>Moreover, known protein complexes are largely incorporated in the assessed modules. Finally, we display the prevalence of our method against modules resulting from other computational approaches.</p> <p>Conclusion</p> <p>The successful integration of heterogeneous data and the concept of the proposed algorithm provide confident functional modules. We also proved that our approach is superior to methods restricted to PPI data only.</p

CSES Module 3 Full Release

The module was administered as a post-election interview. The resulting data are provided along with voting, demographic, district and macro variables in a single dataset. CSES Variable List The list of variables is being provided on the CSES Website to help in understanding what content is available from CSES, and to compare the content available in each module. Themes: MICRO-LEVEL DATA: Identification and study administration variables: weighting factors; election type; date of election 1st and 2nd round; study timing (post election study, pre-election and post-election study, between rounds of majoritarian election); mode of interview; gender of interviewer; date questionnaire administered; primary electoral district of respondent; number of days the interview was conducted after the election Demography: age; gender; education; marital status; union membership; union membership of others in household; business association membership, farmers´ association membership; professional association membership; current employment status; main occupation; socio economic status; employment type - public or private; industrial sector; current employment status, occupation, socio economic status, employment type - public or private, and industrial sector of spouse; household income; number of persons in household; number of children in household under the age of 18; attendance at religious services; religiosity; religious denomination; language usually spoken at home; race; ethnicity; region of residence; rural or urban residence Survey variables: most important issues of election; candidates competencies to deal with most important issues; difference who is in power and who people vote for; evaluation of governments performance; party and leader that represent respondent´s view best; sympathy scale for selected parties and political leaders; assessment of parties and political leaders on a left-right-scale; self-assessment on a left-right-scale; differences of choice options; campaign involvement; satisfaction with democracy; party identification; intensity of party identification; respondent cast a ballot at the current and the previous election; vote choice (presidential, lower house and upper house elections) at the current and the previous election; respondent cast candidate preference vote at the current and the previous election; political information items DISTRICT-LEVEL DATA: number of seats contested in electoral district; number of candidates; number of party lists; percent vote of different parties; official voter turnout in electoral district MACRO-LEVEL DATA: election outcomes by parties in current (lower house/upper house) legislative election; percent of seats in lower house received by parties in current lower house/upper house election; percent of seats in upper house received by parties in current lower house/upper house election; percent of votes received by presidential candidate of parties in current elections; electoral turnout; party of the president and the prime minister before and after the election; number of portfolios held by each party in cabinet, prior to and after the most recent election; size of the cabinet after the most recent election; number of parties participating in election; ideological families of parties; left-right position of parties assigned by experts and alternative dimensions; most salient factors in the election; fairness of the election; formal complaints against national level results; election irregularities reported; scheduled and held date of election; irregularities of election date; extent of election violence and post election violence; geographic concentration of violence; post-election protest; electoral alliances permitted during the election campaign; existing electoral alliances; requirements for joint party lists; possibility of apparentement and types of apparentement agreements; multi-party endorsements on ballot; votes cast; voting procedure; voting rounds; party lists close, open, or flexible; transferable votes; cumulated votes if more than one can be cast; compulsory voting; party threshold; unit for the threshold; freedom house rating; democracy-autocracy polity IV rating; age of the current regime; regime: type of executive; number of months since last lower house and last presidential election; electoral formula for presidential elections; electoral formula in all electoral tiers (majoritarian, proportional or mixed); for lower and upper houses was coded: number of electoral segments; linked electoral segments; dependent formulae in mixed systems; subtypes of mixed electoral systems; district magnitude (number of members elected from each district); number of secondary and tertiary electoral districts; fused vote; size of the lower house; GDP growth (annual percent); GDP per capita; inflation, GDP Deflator (annual percent); Human development index; total population; total unemployment; constitutional federal structure; number of legislative chambers; electoral results data available; effective number of electoral and parliamentary partie

Application of Modified Atmosphere Packaging and Active/Smart Technologies to Red Meat and Poultry: A Review

This paper reviews the current advances in modified atmosphere packaging (MAP) of red meat and poultry products. This type of packaging results in shelf-life prolongation by inhibiting microbial growth and promoting oxidative stability, compared to those packaged aerobically. High O 2 modified atmosphere packaging results in the desirable red colour, but it also enhances both lipid and pigment oxidation and promotes the growth of aerobic spoilage microorganisms. The presence of high levels of CO 2 in modified atmosphere packages inhibits microbial growth but can also cause meat discoloration through oxidation. Low O 2 MAP atmospheres limit microbial growth but change the colour of meat to purple. The use of CO gives promising results due to its positive effects on colour and microorganism growth inhibitions which result in shelf-life prolongation during wider distribution of case-ready products. The use of MAP can lead to an effective growth reduction of pathogenic microorganisms like Listeria sp. and Salmonella sp. The combination of MAP and vacuum with other treatments can be an effective tool in delivering safe minimally processed foodstuffs. In response to the changes in consumer demand and market trends, the area of active and intelligent/smart packaging is becoming more and more important. These relatively new technologies are capable of providing better results regarding product safety and shelf-life prolongation as well as communicating information on several quality characteristics of packaged food during transportation and storage. © 2012 Springer Science+Business Media, LLC

CSES Module 3 Full Release

The module was administered as a post-election interview. The resulting data are provided along with voting, demographic, district and macro variables in a single dataset. CSES Variable List The list of variables is being provided on the CSES Website to help in understanding what content is available from CSES, and to compare the content available in each module. Themes: MICRO-LEVEL DATA: Identification and study administration variables: weighting factors; election type; date of election 1st and 2nd round; study timing (post election study, pre-election and post-election study, between rounds of majoritarian election); mode of interview; gender of interviewer; date questionnaire administered; primary electoral district of respondent; number of days the interview was conducted after the election Demography: age; gender; education; marital status; union membership; union membership of others in household; business association membership, farmers´ association membership; professional association membership; current employment status; main occupation; socio economic status; employment type - public or private; industrial sector; current employment status, occupation, socio economic status, employment type - public or private, and industrial sector of spouse; household income; number of persons in household; number of children in household under the age of 18; attendance at religious services; religiosity; religious denomination; language usually spoken at home; race; ethnicity; region of residence; rural or urban residence Survey variables: most important issues of election; candidates competencies to deal with most important issues; difference who is in power and who people vote for; evaluation of governments performance; party and leader that represent respondent´s view best; sympathy scale for selected parties and political leaders; assessment of parties and political leaders on a left-right-scale; self-assessment on a left-right-scale; differences of choice options; campaign involvement; satisfaction with democracy; party identification; intensity of party identification; respondent cast a ballot at the current and the previous election; vote choice (presidential, lower house and upper house elections) at the current and the previous election; respondent cast candidate preference vote at the current and the previous election; political information items DISTRICT-LEVEL DATA: number of seats contested in electoral district; number of candidates; number of party lists; percent vote of different parties; official voter turnout in electoral district MACRO-LEVEL DATA: election outcomes by parties in current (lower house/upper house) legislative election; percent of seats in lower house received by parties in current lower house/upper house election; percent of seats in upper house received by parties in current lower house/upper house election; percent of votes received by presidential candidate of parties in current elections; electoral turnout; party of the president and the prime minister before and after the election; number of portfolios held by each party in cabinet, prior to and after the most recent election; size of the cabinet after the most recent election; number of parties participating in election; ideological families of parties; left-right position of parties assigned by experts and alternative dimensions; most salient factors in the election; fairness of the election; formal complaints against national level results; election irregularities reported; scheduled and held date of election; irregularities of election date; extent of election violence and post election violence; geographic concentration of violence; post-election protest; electoral alliances permitted during the election campaign; existing electoral alliances; requirements for joint party lists; possibility of apparentement and types of apparentement agreements; multi-party endorsements on ballot; votes cast; voting procedure; voting rounds; party lists close, open, or flexible; transferable votes; cumulated votes if more than one can be cast; compulsory voting; party threshold; unit for the threshold; freedom house rating; democracy-autocracy polity IV rating; age of the current regime; regime: type of executive; number of months since last lower house and last presidential election; electoral formula for presidential elections; electoral formula in all electoral tiers (majoritarian, proportional or mixed); for lower and upper houses was coded: number of electoral segments; linked electoral segments; dependent formulae in mixed systems; subtypes of mixed electoral systems; district magnitude (number of members elected from each district); number of secondary and tertiary electoral districts; fused vote; size of the lower house; GDP growth (annual percent); GDP per capita; inflation, GDP Deflator (annual percent); Human development index; total population; total unemployment; constitutional federal structure; number of legislative chambers; electoral results data available; effective number of electoral and parliamentary partie

CSES Module 1-3 Harmonized Trend File

Für weitere Informationen zur Variablenliste siehe die Dokumentation (Codebook) des CSES Module 1-3 Harmonized Trend File. Informationen zum Inhalt können den Studiennummern ZA5179 CSES Module 1 Full Release, ZA5180 CSES Module 2 Full Release, und ZA5181 CSES Module 3 Full Release entnommen werden