KinMutBase, a database of human disease-causing protein kinase mutations

KinMutBase (http://www.uta.fi/laitokset/imt/KinMut Base.html) is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signalling molecules, in which mutations can lead into diseases including, e.g., immunodeficiencies, cancers and endocrine disorders. The first release of KinMutBase contains information for nine protein tyrosine kinases. There are altogether 170 entries representing 273 families and 403 patients. Mutations appear both in conserved hallmark residues of the kinases as well as in non-homologous sites. The KinMutBase WWW pages provide plenty of information, namely mutation statistics and display, clickable sequences with mutations, restriction enzyme patterns and online submission.     

Computer Hobbyists and the Gaming Industry in Finland

Since the 1950s, digital games in Finland have bridged gaps between professional users and the public as well as institutional and domestic environments. The early significance of Finland's 1970s and 1980s computer games hobbyist and hacker cultures is still evident: clear connections exist between the country's rich history of such subcultures and its modern international success in multimedia and mobile entertainment.     

Ionic Liquids for Chloromethane/Isobutane Distillative Separation: Express Screening

The present study centres on room‐temperature ionic liquids (ILs) as entrainers in extractive distillation of chloromethane/isobutane mixtures. The binary system, chloromethane/isobutene, is an azeotropic system. In this study, IL entrainers are shown to be able to break the azeotrope and, thus, assure the separation in the whole range of chloromethane/isobutane ratios. ILs formed from different cations and anions are considered and their influence on chloromethane/isobutane separation is explored. Among the ILs studied, those containing the trifluoromethanesulfonate ([CF₃SO₃]^–) or tricyanomethanide ([C(CN)₃]^–) anion are demonstrated to exhibit an enhanced potential for chloromethane/isobutane separation compared to the corresponding ILs based on the bis(trifluoromethylsulfonyl)imide ([Tf₂N]^–) anion. Moreover, the ILs enclosing these anions are cheaper than those with the [Tf₂N]^– anion. Thus, the separation ability, solubility of chloromethane/isobutane mixtures, and costs of IL entrainers can be adjusted by the right choice of cations and anions.     

Urban qualities and residents’ strategies in compact global south cities: the case of Havana

Research and policy argue for more compact cities to respond to sustainable development challenges. However, what actually needs to be made more compact and how, is under examined, particularly in global South cities where north notions of urban qualities are adopted without being questioned. Informed by a qualitative study in informal and compact neighborhoods in Havana, this paper explores which qualities are important to deliver more just cities, and what strategies are developed by residents to strengthen beneficial qualities and address detrimental qualities in contexts of informal urbanization and compactness. It shows how the street, human capital, neighborhood, housing affordability, citizenship and vibrancy are significant compact city qualities neglected in the literature. Finally, the paper shows how diverse strategies are developed by residents to draw upon these qualities, such as self-help urbanism, learning and innovation, economic entrepreneurship, networks of solidarity, economies of reciprocity, local imaginaries and active citizenship.

     

Homological scaffolds of brain functional networks

Networks, as efficient representations of complex systems, have appealed to scientists for a long time and now permeate many areas of science, including neuroimaging (Bullmore and Sporns 2009 Nat. Rev. Neurosci. 10, 186–198. (doi:10.1038/nrn2618)). Traditionally, the structure of complex networks has been studied through their statistical properties and metrics concerned with node and link properties, e.g. degree-distribution, node centrality and modularity. Here, we study the characteristics of functional brain networks at the mesoscopic level from a novel perspective that highlights the role of inhomogeneities in the fabric of functional connections. This can be done by focusing on the features of a set of topological objects—homological cycles—associated with the weighted functional network. We leverage the detected topological information to define the homological scaffolds, a new set of objects designed to represent compactly the homological features of the correlation network and simultaneously make their homological properties amenable to networks theoretical methods. As a proof of principle, we apply these tools to compare resting-state functional brain activity in 15 healthy volunteers after intravenous infusion of placebo and psilocybin—the main psychoactive component of magic mushrooms. The results show that the homological structure of the brain''s functional patterns undergoes a dramatic change post-psilocybin, characterized by the appearance of many transient structures of low stability and of a small number of persistent ones that are not observed in the case of placebo.     

Link quality analysis and measurement in wireless mesh networks

Protocols and applications in wireless mesh networks often optimize their performance by measuring the quality of wireless links. However, measuring and characterizing link-quality is a challenging task due to the nature of wireless channel and device-specific properties of radios. The paper proposes two aspects of link-quality measurement and estimation in realistic networks that benefit higher-layer protocols. First, we analyze the statistical properties of link-quality metrics, such as received signal strength and packet error rates, in an indoor IEEE 802.11 mesh network. We show that the statistical distribution and memory properties vary across different links, but are predictable. The next contribution of the paper is a real-time measurement framework that enables higher-level protocols in wireless mesh networks. We discuss the architectural requirements and our implementation experiences of a measurement framework. In addition, we provide three concrete applications that use the measured link-quality and statistical inference to better adapt their behavior.     

Efficiency of antioxidants in thick-walled natural rubber samples evaluated by differential scanning calorimetry and compression stress–relaxation

The effect ot two antioxidants, IPPD and DENA, on the aging properties of TMTD-vulcanized natural rubber was studied by DSC. In the case of IPPD, the results were compared with mechanical measurements. The DSC measurements were carried out on specimens taken at different depths from cylindrical samples. The decrease in oxidative induction time was less pronounced for IPPD than for DENA at the edge of the samples. In the interior, the opposite behaviour was observed.     

Regulation of adherence and virulence by the Entamoeba histolytica lectin cytoplasmic domain, which contains a beta2 integrin motif

Killing of human cells by the parasite Entamoeba histolytica requires adherence via an amebic cell surface lectin. Lectin activity in the parasite is regulated by inside-out signaling. The lectin cytoplasmic domain has sequence identity with a region of the beta2 integrin cytoplasmic tail implicated in regulation of integrin-mediated adhesion. Intracellular expression of a fusion protein containing the cytoplasmic domain of the lectin has a dominant negative effect on extracellular lectin-mediated cell adherence. Mutation of the integrin-like sequence abrogates the dominant negative effect. Amebae expressing the dominant negative mutant are less virulent in an animal model of amebiasis. These results suggest that inside-out signaling via the lectin cytoplasmic domain may control the extracellular adhesive activity of the amebic lectin and provide in vivo demonstration of the lectin's role in virulence.     

How many measurements are necessary in diagnosing mild to moderate hypertension?

Cowdria ruminantium is the etiologic agent of heartwater, a tick-transmitted foreign animal disease with considerable potential for entrance into the USA. A competitive enzyme-linked immunosorbent assay (cELISA) was developed to detect serologic responses to C. ruminantium infection. The cELISA utilized a recombinant form of the C. ruminantium major antigenic protein (MAP-1) as the antigen and an anti-MAP-1 monoclonal antibody as the competing indicator reagent. Experimental antisera to C. ruminantium and a wide variety of related ehrlichial organisms were used to evaluate cELISA reactivity. Only sera against C. ruminantium, Ehrlichia canis, E. chaffeensis, and a recently discovered cervine ehrlichia-like organism reacted positively in the cELISA. Specificity of the cELISA was > or = 99.5% in a survey of 1,774 southeastern US and Puerto Rican slaughter cattle sera but was only 85% in a group of 79 hunter-killed white-tailed deer (Odocoileus virginianus) from the southeastern USA. Reference true-positive and cELISA false-positive sera were further analyzed by end point titrations using the cELISA and by indirect fluorescent antibody (IFA) tests for reactivity with C. ruminantium, E. canis, and E. chaffeensis antigens. True heartwater-positive sera were significantly more reactive using the cELISA and C. ruminantium IFA procedures (P < 0.05), whereas false-positive sera were significantly more reactive with the antigens used in the E. chaffeensis IFA procedure (P < 0.05). A group of sera from 210 field-origin ruminants residing on known or potentially heartwater-endemic Caribbean islands revealed a substantial (12.4%) prevalence of cELISA-positive specimens. The cELISA is a relatively specific serodiagnostic test for heartwater in cattle and could be used to monitor for possible introduction of the disease into the USA. The cELISA may also be an excellent tool for monitoring the success of an ongoing Caribbean Amblyomma tick eradication program designed to eliminate the biological vector responsible for the perpetuation and spread of this dangerous foreign animal disease.