Data-dependent visualization of biological networks in the web-browser with NDExEdit

Networks are a common methodology used to capture increasingly complex associations between biological entities. They serve as a resource of biological knowledge for bioinformatics analyses, and also comprise the subsequent results. However, the interpretation of biological networks is challenging and requires suitable visualizations dependent on the contained information. The most prominent software in the field for the visualization of biological networks is Cytoscape, a desktop modeling environment also including many features for analysis. A further challenge when working with networks is their distribution. Within a typical collaborative workflow, even slight changes of the network data force one to repeat the visualization step as well. Also, just minor adjustments to the visual representation not only need the networks to be transferred back and forth. Collaboration on the same resources requires specific infrastructure to avoid redundancies, or worse, the corruption of the data. A well-established solution is provided by the NDEx platform where users can upload a network, share it with selected colleagues or make it publicly available. NDExEdit is a web-based application where simple changes can be made to biological networks within the browser, and which does not require installation. With our tool, plain networks can be enhanced easily for further usage in presentations and publications. Since the network data is only stored locally within the web browser, users can edit their private networks without concerns of unintentional publication. The web tool is designed to conform to the Cytoscape Exchange (CX) format as a data model, which is used for the data transmission by both tools, Cytoscape and NDEx. Therefore the modified network can be directly exported to the NDEx platform or saved as a compatible CX file, additionally to standard image formats like PNG and JPEG

The RCX extension hub: a resource for implementations extending the R adaption of the cytoscape exchange format

Public repositories provide access to biological networks for investigations, and subsequently serve to distribute the network encoded biomedical and even clinically relevant results. However, inclusion of complementary information requires data structures and implementations customized to the integrated data for network representation, usage in supporting application, and extending analysis functionality. Partitioning of this information into individual aspects of a network facilitates compatibility and reusability of the network-based results, but also requires support and accessibility of the extensions and their implementations. The RCX extension hub offers overview and access to extensions of the Cytoscape exchange format implemented in R. The hub supports the realization of self-customized extension through guides, example implementations, and a template for the creation of R extension packages

Bibliometric evaluation of the scientific production of the Stomatos Dental Journal

This cross-sectional study aimed to evaluate the abstracts of all articles published in the Stomatos Dental Journal between 1995 and 2009 and to obtain data on the methodological design of each article, the dental specialties focused on, and the authors’ institution of origin. A total of 206 abstracts were reviewed by two independent examiners. The results showed that the most frequent study designs were literature reviews (24.3%), cross-sectional studies (24.3%), laboratory in vitro studies (22.3%), and case reports (18.4%). The dental specialties with the highest number of articles were operative dentistry (16%), endodontics (15.5%), pediatric dentistry (10.7%), and oral and maxillofacial surgery and traumatology (10.2%). Most articles had Universidade Luterana do Brasil (ULBRA/Canoas) as the institution of origin (75.2%). Our findings revealed a pressing need to increase the number of studies with higher levels of evidence in all dental specialties and also to encourage the publication of articles from other institutions in order to qualify the journal

Minimum inhibitory (MIC) and minimum microbicidal concentration (MMC) of polihexanide and triclosan against antibiotic sensitive and resistant Staphylococcus aureus and Escherichia coli strains

Background: An in-vitro study was conducted investigating the antimicrobial efficacy of polihexanide and triclosan against clinical isolates and reference laboratory strains of Staphylococcus aureus and Escherichia coli

Inorganic pyrophosphatase in uncultivable hemotrophic mycoplasmas: identification and properties of the enzyme from Mycoplasma suis

BACKGROUND: Mycoplasma suis belongs to a group of highly specialized hemotrophic bacteria that attach to the surface of host erythrocytes. Hemotrophic mycoplasmas are uncultivable and the genomes are not sequenced so far. Therefore, there is a need for the clarification of essential metabolic pathways which could be crucial barriers for the establishment of an in vitro cultivation system for these veterinary significant bacteria.Inorganic pyrophosphatases (PPase) are important enzymes that catalyze the hydrolysis of inorganic pyrophosphate PPi to inorganic phosphate Pi. PPases are essential and ubiquitous metal-dependent enzymes providing a thermodynamic pull for many biosynthetic reactions. Here, we describe the identification, recombinant production and characterization of the soluble (s)PPase of Mycoplasma suis. RESULTS: Screening of genomic M. suis libraries was used to identify a gene encoding the M. suis inorganic pyrophosphatase (sPPase). The M. suis sPPase consists of 164 amino acids with a molecular mass of 20 kDa. The highest identity of 63.7% was found to the M. penetrans sPPase. The typical 13 active site residues as well as the cation binding signature could be also identified in the M. suis sPPase. The activity of the M. suis enzyme was strongly dependent on Mg2+ and significantly lower in the presence of Mn2+ and Zn2+. Addition of Ca2+ and EDTA inhibited the M. suis sPPase activity. These characteristics confirmed the affiliation of the M. suis PPase to family I soluble PPases. The highest activity was determined at pH 9.0. In M. suis the sPPase builds tetramers of 80 kDa which were detected by convalescent sera from experimentally M. suis infected pigs. CONCLUSION: The identification and characterization of the sPPase of M. suis is an additional step towards the clarification of the metabolism of hemotrophic mycoplasmas and, thus, important for the establishment of an in vitro cultivation system. As an antigenic and conserved protein the M. suis sPPase could in future be further analyzed as a diagnostic antigen

Small x resummation of rapidity distributions: the case of Higgs production

We provide a method for the all order computation of small x contributions at the leading logarithmic level to cross-sections which are differential in rapidity. The method is based on a generalization to rapidity distributions of the high energy (or k_T) factorization theorem hitherto proven for inclusive cross-sections. We apply the method to Higgs production in gluon-gluon fusion, both with finite top mass and in the infinite mass limit: in both cases, we determine all-order resummed expressions, as well as explicit expressions for the leading small x terms up to NNLO. We use our result to construct an explicit approximate analytic expression of the finite-mass NLO rapidity distribution and an estimate of finite-mass corrections at NNLO.Comment: 53 pages, 6 figures. Several typos corrected. Final version, to be published in NP

Immunomodulation to Prevent or Treat Neonatal Sepsis: Past, Present, and Future

Despite continued advances in neonatal medicine, sepsis remains a leading cause of death worldwide in neonatal intensive care units. The clinical presentation of sepsis in neonates varies markedly from that in older children and adults, and distinct acute inflammatory responses results in age-specific inflammatory and protective immune response to infection. This review first provides an overview of the neonatal immune system, then covers current mainstream, and experimental preventive and adjuvant therapies in neonatal sepsis. We also discuss how the distinct physiology of the perinatal period shapes early life immune responses and review strategies to reduce neonatal sepsis-related morbidity and mortality. A summary of studies that characterize immune ontogeny and neonatal sepsis is presented, followed by discussion of clinical trials assessing interventions such as breast milk, lactoferrin, probiotics, and pentoxifylline. Finally, we critically appraise future treatment options such as stem cell therapy, other antimicrobial protein and peptides, and targeting of pattern recognition receptors in an effort to prevent and/or treat sepsis in this highly vulnerable neonatal population

Publication Trends Studies Involving Disabled Persons with Dental Care Needs: A 20-Year Bibliometric Analysis

Objective: To evaluate scientific production on disabled persons with dental care needs over a 20-year period. Material and Methods: The search was conducted in the PubMed database using the MeSH terms “Disabled Persons” AND “Dentistry”. Three researchers selected articles based on readings of the title, abstract and full text. The articles were categorized according to periodical, country, study design, subject and classification of comorbidities and associated disorders. Three hundred ninety-seven articles published in 140 periodicals were included. Results: The periodicals Special Care in Dentistry (54), Dental Clinics of North America (14) and British Dental Journal (14) accounted for 21% of the publications. The studies were conducted in 50 countries, with the United States accounting for 33%. More than half (52%) of the studies had a cross-sectional design. The main subject addressed was oral diagnosis and most of the comorbidities were generalized disabilities. Conclusion: Although a large number of the periodicals have contributed to knowledge building on disabled persons with dental care needs, the number of articles is small compared to other fields of dentistry. Moreover, important gaps in knowledge persist and projects with better methodological designs are needed to offer a more substantial contribution to clinical practice

A commonly used rumen-protected conjugated linoleic acid supplement marginally affects fatty acid distribution of body tissues and gene expression of mammary gland in heifers during early lactation

Background: Conjugated linoleic acids (CLA) in general, and in particular the trans-10, cis-12 (t10, c12-CLA) isomer are potent modulators of milk fat synthesis in dairy cows. Studies in rodents, such as mice, have revealed that t10, c12-CLA is responsible for hepatic lipodystrophy and decreased adipose tissue with subsequent changes in the fatty acid distribution. The present study aimed to investigate the fatty acid distribution of lipids in several body tissues compared to their distribution in milk fat in early lactating cows in response to CLA treatment. Effects in mammary gland are further analyzed at gene expression level. Methods: Twenty-five Holstein heifers were fed a diet supplemented with (CLA groups) or without (CON groups) a rumen-protected CLA supplement that provided 6 g/d of c9, t11-and t10, c12-CLA. Five groups of randomly assigned cows were analyzed according to experimental design based on feeding and time of slaughter. Cows in the first group received no CLA supplement and were slaughtered one day postpartum (CON0). Milk samples were taken from the remaining cows in CON and CLA groups until slaughter at 42 (period 1) and 105 (period 2) days in milk (DIM). Immediately after slaughter, tissue samples from liver, retroperitoneal fat, mammary gland and M. longissimus (13th rib) were obtained and analyzed for fatty acid distribution. Relevant genes involved in lipid metabolism of the mammary gland were analyzed using a custom-made microarray platform. Results: Both supplemented CLA isomers increased significantly in milk fat. Furthermore, preformed fatty acids increased at the expense of de novo-synthesized fatty acids. Total and single trans-octadecenoic acids (e. g., t10-18:1 and t11-18:1) also significantly increased. Fatty acid distribution of the mammary gland showed similar changes to those in milk fat, due mainly to residual milk but without affecting gene expression. Liver fatty acids were not altered except for trans-octadecenoic acids, which were increased. Adipose tissue and M. longissimus were only marginally affected by CLA supplementation. Conclusions: Daily supplementation with CLA led to typical alterations usually observed in milk fat depression (reduction of de novo-synthesized fatty acids) but only marginally affected tissue lipids. Gene expression of the mammary gland was not influenced by CLA supplementation