Non-essential genes form the hubs of genome scale protein function and environmental gene expression networks in Salmonella enterica serovar Typhimurium

Background Salmonella Typhimurium is an important pathogen of human and animals. It shows a broad growth range and survives in harsh conditions. The aim of this study was to analyze transcriptional responses to a number of growth and stress conditions as well as the relationship of metabolic pathways and/or cell functions at the genome-scale-level by network analysis, and further to explore whether highly connected genes (hubs) in these networks were essential for growth, stress adaptation and virulence. Results De novo generated as well as published transcriptional data for 425 selected genes under a number of growth and stress conditions were used to construct a bipartite network connecting culture conditions and significantly regulated genes (transcriptional network). Also, a genome scale network was constructed for strain LT2. The latter connected genes with metabolic pathways and cellular functions. Both networks were shown to belong to the family of scale-free networks characterized by the presence of highly connected nodes or hubs which are genes whose transcription is regulated when responding to many of the assayed culture conditions or genes encoding products involved in a high number of metabolic pathways and cell functions. The five genes with most connections in the transcriptional network (wraB, ygaU, uspA, cbpA and osmC) and in the genome scale network (ychN, siiF (STM4262), yajD, ybeB and dcoC) were selected for mutations, however mutagenesis of ygaU and ybeB proved unsuccessful. No difference between mutants and the wild type strain was observed during growth at unfavorable temperatures, pH values, NaCl concentrations and in the presence of H2O2. Eight mutants were evaluated for virulence in C57/BL6 mice and none differed from the wild type strain. Notably, however, deviations of phenotypes with respect to the wild type were observed when combinations of these genes were deleted. Conclusion Network analysis revealed the presence of hubs in both transcriptional and functional networks of S. Typhimurium. Hubs theoretically confer higher resistance to random mutation but a greater susceptibility to directed attacks, however, we found that genes that formed hubs were dispensable for growth, stress adaptation and virulence, suggesting that evolution favors non-essential genes as main connectors in cellular networks

Approximation algorithms for NEXTtime-hard periodically specified problems and domino problems

We study the efficient approximability of two general class of problems: (1) optimization versions of the domino problems studies in [Ha85, Ha86, vEB83, SB84] and (2) graph and satisfiability problems when specified using various kinds of periodic specifications. Both easiness and hardness results are obtained. Our efficient approximation algorithms and schemes are based on extensions of the ideas. Two of properties of our results obtained here are: (1) For the first time, efficient approximation algorithms and schemes have been developed for natural NEXPTIME-complete problems. (2) Our results are the first polynomial time approximation algorithms with good performance guarantees for `hard` problems specified using various kinds of periodic specifications considered in this paper. Our results significantly extend the results in [HW94, Wa93, MH+94]

Periodically specified satisfiability problems with applications: An alternative to domino problems

We characterize the complexities of several basic generalized CNF satisfiability problems SAT(S), when instances are specified using various kinds of 1- and 2-dimensional periodic specifications. We outline how this characterization can be used to prove a number of new hardness results for the complexity classes DSPACE(n), NSPACE(n), DEXPTIME, NEXPTIME, EXPSPACE etc. The hardness results presented significantly extend the known hardness results for periodically specified problems. Several advantages axe outlined of the use of periodically specified satisfiability problems over the use of domino problems in proving both hardness and easiness results. As one corollary, we show that a number of basic NP-hard problems become EXPSPACE hard when inputs axe represented using 1-dimensional infinite periodic wide specifications. This answers a long standing open question posed by Orlin

Multiple publications: The main reason for the retraction of papers in computer science

This paper intends to review the reasons for the retraction over the last decade. The paper particularly aims at reviewing these reasons with reference to computer science field to assist authors in comprehending the style of writing. To do that, a total of thirty-six retracted papers found on the Web of Science within Jan 2007 through July 2017 are explored. Given the retraction notices which are based on ten common reasons, this paper classifies the two main categories, namely random and nonrandom retraction. Retraction due to the duplication of publications scored the highest proportion of all other reasons reviewed

Sequential dynamical systems with threshold functions.

A sequential dynamical system (SDS) (see [BH+01] and the references therein) consists of an undirected graph G(V,E) where each node {nu} {epsilon} V is associated with a Boolean state (s{sub {nu}}) and a symmetric Boolean function f{sub {nu}} (called the local transition function at {nu}). The inputs to f{sub {nu}} are s{sub {nu}} and the states of all the nodes adjacent to {nu}. In each step of the SDS, the nodes update their state values using their local transition functions in the order specified by a given permutation {pi} of the nodes. A configuration of the SDS is an n-tuple (b{sub 1}, b{sub 2}...,b{sub n}) where n = |V| and b{sub i} {epsilon} {l_brace}0,1{r_brace} is the state value of node {nu}{sub i}. The system starts in a specified initial configuration and each step of the SDS produces a (possibly new) configuration

Using Vignettes in Qualitative Research to Explore Barriers and Facilitating Factors to the Uptake of Prevention of Mother-to-Child Transmission Services in Rural Tanzania: A Critical Analysis.

Vignettes are short stories about a hypothetical person, traditionally used within research (quantitative or qualitative) on sensitive topics in the developed world. Studies using vignettes in the developing world are emerging, but with no critical examination of their usefulness in such settings. We describe the development and application of vignettes to a qualitative investigation of barriers to uptake of prevention of mother-to-child transmission (PMTCT) HIV services in rural Tanzania in 2012, and critique the successes and challenges of using the technique in this setting. Participatory Learning and Action (PLA) group activities (3 male; 3 female groups from Kisesa, north-west Tanzania) were used to develop a vignette representing realistic experiences of an HIV-infected pregnant woman in the community. The vignette was discussed during in-depth interviews with 16 HIV-positive women, 3 partners/relatives, and 5 HIV-negative women who had given birth recently. A critical analysis was applied to assess the development, implementation and usefulness of the vignette. The majority of in-depth interviewees understood the concept of the vignette and felt the story was realistic, although the story or questions needed repeating in some cases. In-depth interviewers generally applied the vignette as intended, though occasionally were unsure whether to steer the conversation back to the vignette character when participants segued into personal experiences. Interviewees were occasionally confused by questions and responded with what the character should do rather than would do; also confusing fieldworkers and presenting difficulties for researchers in interpretation. Use of the vignette achieved the main objectives, putting most participants at ease and generating data on barriers to PMTCT service uptake. Participants' responses to the vignette often reflected their own experience (revealed later in the interviews). Participatory group research is an effective method for developing vignettes. A vignette was incorporated into qualitative interview discussion guides and used successfully in rural Africa to draw out barriers to PMTCT service use; vignettes may also be valuable in HIV, health service use and drug adherence research in this setting. Application of this technique can prove challenging for fieldworkers, so thorough training should be provided prior to its use

Multiple publications: The main reason for the retraction of papers in computer science

This paper intends to review the reasons for the retraction over the last decade. The paper particularly aims at reviewing these reasons with reference to computer science field to assist authors in comprehending the style of writing. To do that, a total of thirty-six retracted papers found on the Web of Science within Jan 2007 through July 2017 are explored. Given the retraction notices which are based on ten common reasons, this paper classifies the two main categories, namely random and nonrandom retraction. Retraction due to the duplication of publications scored the highest proportion of all other reasons reviewed