Scientific workflows for bibliometrics

Scientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They are also favorable in terms of reusability, as previously designed workflows could be made publicly available through the myExperiment community and then used in other workflows. We here illustrate how scientific workflows and the Taverna workbench in particular can be used in bibliometrics. We discuss the specific capabilities of Taverna that makes this software a powerful tool in this field, such as automated data import via Web services, data extraction from XML by XPaths, and statistical analysis and visualization with R. The support of the latter is particularly relevant, as it allows integration of a number of recently developed R packages specifically for bibliometrics. Examples are used to illustrate the possibilities of Taverna in the fields of bibliometrics and scientometrics

Protein expression dynamics during Escherichia Coli glucose-lactose diauxie

BACKGROUND: Escherichia coli is a well-studied anaerobic bacteria which is able to regulate metabolic pathways depending on the type of sugar presented in the medium. We have studied the glucose-lactose shift in E. coli at the protein level using a recently developed mass spectrometry platform. METHOD: Cells were grown in minimal medium containing two sugars (glucose and lactose) and analyzed using novel mass spectrometry cluster. The cluster combines the high resolving power and dynamic range of Fourier transform ion cyclotron resonance (FTICR) for accurate mass measurement and quantitation with multiple ion traps for fast and sensitive tandem mass spectrometry. The protein expression profile was followed in time across the glucose-lactose diauxic shift using label-free quantitation from the FTICR data. RESULTS AND CONCLUSION: The entire dataset was interrogated by KEGG pathway analysis, mapping measured changes in protein abundance onto known metabolic pathways. The obtained results were consistent with previously published gene expression data, with β-galactosidase being the most strongly induced protein during the diauxic shift

Scientific workflows for bibliometrics

Scientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They are also favorable in terms of reusability, as previously designed workflows could be made publicly available through the myExperiment community and then used in other workflows. We here illustrate how scientific workflows and the Taverna workbench in particular can be used in bibliometrics. We discuss the specific capabilities of Taverna that makes this software a powerful tool in this field, such as automated data import via Web services, data extraction from XML by XPaths, and statistical analysis and visualization with R. The support of the latter is particularly relevant, as it allows integration of a number of recently developed R packages specifically for bibliometrics. Examples are used to illustrate the possibilities of Taverna in the fields of bibliometrics and scientometrics.Proteomic

Diagnostics and ideology

The purpose of this article is to examine current theories and concepts concerning children with concentration difficulties and hyper-activity from a perspective of the sociology of knowledge. The material on which the study is based is popular science writing on the subject. The examination reveals theories and concepts, which carry definite traits of socio-pathological thought. The danger of social pathology becoming an ideology furthering conformity is discussed. Finally a sketch of a model of understanding, which has as its starting point deviant behavior as a carrier of social meaning, is drawn

Theoretical considerations for next-generation proteomics

While mass spectrometry still dominates proteomics research, alternative and potentially disruptive, next-generation technologies are receiving increased investment and attention. Most of these technologies aim at the sequencing of single peptide or protein molecules, typically labeling or otherwise distinguishing a subset of the proteinogenic amino acids. This note considers some theoretical aspects of these future technologies from a bottom-up proteomics viewpoint, including the ability to uniquely identify human proteins as a function of which and how many amino acids can be read, enzymatic efficiency, and the maximum read length. This is done through simulations under ideal and non-ideal conditions to set benchmarks for what may be achievable with future single-molecule sequencing technology. The simulations reveal, among other observations, that the best choice of reading N amino acids performs similarly to the average choice of N+1 amino acids, and that the discrimination power of the amino acids scales with their frequency in the proteome. The simulations are agnostic with respect to the next-generation proteomics platform, and the results and conclusions should therefore be applicable to any single-molecule partial peptide sequencing technology.Proteomic

Surface activity and film formation from the surface associated material of artificial surfactant preparations

AbstractSurfactant proteins B and C (SP-B and SP-C) are present in natural derived surfactant preparations used for treatment of respiratory distress syndrome. Herein the surface activity of an SP-C analogue (SP-C(LKS)), a hybrid peptide between SP-C and bacteriorhodopsin (SP-C/BR) and a model peptide (KL4) was studied with a captive bubble surfactometer (CBS). The peptides were mixed with either 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)/phosphatidylglycerol (PG) (7:3, by weight) or DPPC/PG/palmitic acid (68:22:9, by weight) at a concentration of 1 mg/ml in HEPES buffer, pH 6.9 and a polypeptide/lipid weight ratio of 0.02–0.03. In some lipid/peptide preparations also 2% of SP-B was included. Adsorption, monitored as surface tension vs. time for 10 min after bubble formation did not show discernible differences for the whole set of preparations. Equilibrium surface tensions of approximately 25 mN/m were reached after 5–10 min for all preparations, although those with SP-C/BR appeared not to reach end point of adsorption within 10 min. Area compression needed to reach minimum surface tension of 0.5–2.0 mN/m was least for the KL4 preparation, about 13% in the first cycle. 3% SP-C(LKS) in DPPC:PG (7:3, by weight) reached minimum surface tension upon 27% compression in the first cycle. If DPPC:PG:PA (68:22:9, by weight) was used instead only 16% area compression was needed and 14% if also 2% SP-B was included. 3% SP-C(LKS) in DPPC:PG (7:3, by weight)+2% SP-B needed 34% compression to reach minimum surface tension. The replenishment of material from a surface associated surfactant reservoir was estimated with subphase depletion experiments. With the 2% KL4 preparation incorporation of excess material took place at a surface tension of 25–35 mN/m during stepwise bubble expansion and excess material equivalent to 4.3 monolayers was found. When 2% SP-B was added to 3% SP-C(LKS) in DPPC:PG (7:3, by weight) the number of excess monolayers increased from 1.5 to 3.6 and the incorporation took place at 30–40 mN/m. When SP-B was added to 3% SP-C(LKS) in DPPC:PG:PA (68:22:9, by weight) the number of excess monolayers increased from 0.5 to 3.4 and incorporation took place at 40–50 mN/m. With 2% SP-C/BR incorporation took place at 40–45 mN/m, frequent instability clicks were observed and excess material of approximately 1.1 monolayer was estimated

In Conversation with Mubin Shaikh: From Salafi Jihadist to Undercover Agent inside the "Toronto 18" Terrorist Group

This interview with former undercover agent Mubin Shaikh can help academics and security practitioners understand the key role played and the challenges faced by covert human intelligence sources within domestic terrorist groups. The interview highlights the identity crisis, the personal factors, and the allure of jihadi militancy that initially drove Shaikh to join a Salafi jihadist group. It investigates Shaikh’s process of disengagement from the Salafi jihadist belief system and his rediscovery of a moderate, inclusive, and benevolent form of Islam. It explores his work as an undercover agent for the Canadian Security Intelligence Service, the Royal Canadian Mounted Police, and the Integrated National Security Enforcement Team responsible for disrupting domestic terrorist groups. The “Toronto 18” terrorist cell, the key role played by undercover agents in preventing terrorist action, and the challenges posed by entrapment are also discussed

Rewinding the molecular clock: looking at pioneering molecular phylogenetics experiments in the light of proteomics

Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a "gem" at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants.Proteomic