Finding lowest common ancestors in arbitrarily directed trees

It is well known how to preprocess a rooted tree in linear time to yield the lowest common ancestor of any given pair of nodes in constant time. We generalize these algorithms for graphs called Arbitrarily Directed Trees, or ADTs. Such trees are obtained by reversing the directions of some edges in trees with the customary “root-to-leaf” orientation of edges.     

A cloned human germ cell tumor-derived cell line differentiating in culture

We have derived a clonal cell line (HGCT-1) from a lymph node metastasis of a primary testicular germ cell tumor (GCT). The tumor was negative for the embryonal carcinoma (EC) cell marker BerH2 but positive for vimentin, cytokeratin (CK) and desmin. Comparative genomic hybridization (CGH) revealed a high-level amplification at 12p that was observed in both the metastatic tumor and in the cultured HGCT-1 cells. In vitro, the phenotype of HGCT-1 cells was modulated by the culture conditions. In the presence of 10% fetal calf serum (FCS), the majority of HGCT-1 cells lacked CK and desmin. If cultured in 0.5% FCS, HGCT-1 cells acquired a uniform co-expression of vimentin, CK and desmin. Upon treatment with retinoic acid (RA), HGCT-1 cells lost the expression of desmin, but exhibited abundant CK filaments. Simultaneously, they started to express desmoplakin, form desmosomes and flatten on the culture substratum. The RA-induced changes were irreversible, whereas those following the culture in 0.5% FCS were at least partially reversible. When xenografted into an immunosuppressed rat, HGCT-1 cells formed a tumor consisting of epithelial- and mesenchymal-like structures. HGCT-1 cells thus represent a pluripotential cell system with a capacity for reversible phenotypic modulation and for irreversible differentiation into epithelial-type cells. The behavior of this novel cell line, distinct from established EC cell models, suggests a complex regulation of GCT cell differentiation.     

Binding of quinacrine to acidic phospholipids and pancreatic phospholipase A2. Effects on the catalytic activity of the enzyme

Binding of quinacrine to phospholipids and porcine pancreatic phospholipase A2 (PLA2) was investigated using fluorescence resonance energy transfer, Langmuir films, assay for the enzymatic activity, and molecular modeling. No significant binding of this drug to the zwitterionic phosphatidylcholine was observed whereas a high affinity for acidic phospholipids was revealed by quenching of pyrene-labeled phospholipid analogues. Partial reversal of this binding was observed due to the addition of 4 mM CaCl2. Quinacrine efficiently and independently of the lipid surface pressure penetrated into monolayers of phosphatidylglycerol while only a weak penetration into phosphatidylcholine films was evident. Quinacrine also bound to eosin-labeled PLA2, and the addition of 4 mM CaCl2 reversed this interaction almost completely. In the presence of acidic phospholipids both the drug and the enzyme were attached to the lipid surface. Studies on the influence of quinacrine on the activity of PLA2 toward pyrene-labeled phospholipid analogues revealed that the hydrolysis of phosphatidylcholine was progressively reduced as a function of increasing [quinacrine]. At low [CaCl2] and low quinacrine:lipid molar ratios (<1:5) quinacrine enhanced slightly the rate of hydrolysis of acidic phospholipids whereas at higher drug:lipid molar ratios (>1:2) an inhibition was observed. In the presence of 1 mM CaCl2 quinacrine inhibited PLA2-catalyzed hydrolysis of phosphatidylglycerol only when the drug:lipid molar ratio exceeded 1:1. The presence of 4 mM CaCl2 abolished nearly completely the inhibition with all the substrate analogues used. Our data suggest that the inhibition of PLA2 by quinacrine is due to its binding to the enzyme. This is supported also by molecular modeling which suggested a binding site for quinacrine close to the active site and Ca2+ binding site of the enzyme. Importantly, our data indicate that quinacrine binds avidly to acidic phospholipids and their presence may influence the drug-enzyme interaction and the inhibition of the enzyme action. Accordingly, presence of quinacrine may interfere also with other processes that require the presence of acidic lipids and/or Ca2+, such as the function of the nicotinic acetylcholine receptor.     

IEEE 802.11ac MIMO Transceiver Baseband Processing on a VLIW Processor

Wireless standards are evolving rapidly due to the exponential growth in the number of portable devices along with the applications with high data rate requirements. Adaptable software based signal processing implementations for these devices can make the deployment of the constantly evolving standards faster and less expensive. The flagship technology from the IEEE WLAN family, the IEEE 802.11ac, aims at achieving very high throughputs in local area connectivity scenarios. This article presents a software based implementation for the Multiple Input and Multiple Output (MIMO) transmitter and receiver baseband processing conforming to the IEEE 802.11ac standard which can achieve transmission bit rates beyond 1Gbps. This work focuses on the Physical layer frequency domain processing. Various configurations, including 2×2 and 4×4 MIMO are considered for the implementation. To utilize the available data and instruction level parallelism, a DSP core with vector extensions is selected as the implementation platform. Then, the feasibility of the presented software-based solution is assessed by studying the number of clock cycles and power consumption of the different scenarios implemented on this core. Such Software Defined Radio based approaches can potentially offer more flexibility, high energy efficiency, reduced design efforts and thus shorter time-to-market cycles in comparison with the conventional fixed-function hardware methods.     

Climate change,energy security,and risk—debating nuclear new build in Finland,France and the UK

Concerns about climate change and energy security have been major arguments used to justify the recent return of nuclear power as a serious electricity generation option in various parts of the world. This article examines the recent public discussion in Finland, France, and the UK – three countries currently in the process of constructing or planning new nuclear power stations. To place the public discussion on nuclear power within the relationship between policy discourses and contexts, the article addresses three interrelated themes: the justifications and discursive strategies employed by nuclear advocates and critics, the similarities and differences in debates between the three countries, and the interaction between the country-specific state orientations and the argumentation concerning nuclear power. Drawing from documentary analysis and semi-structured interviews, the article identifies and analyses key discursive strategies and their use in the context of the respective state orientations: ‘technology-and-industry-know-best’ in Finland, ‘government-knows-best’ in France, and ‘markets-know-best’ in the UK. The nuclear debates illustrate subtle ongoing transformations in these orientations, notably in the ways in which the relations between markets, the state, and civil society are portrayed in the nuclear debates.     

Synthesis of graphene nanoribbons encapsulated in single-walled carbon nanotubes

A novel material, graphene nanoribbons encapsulated in single-walled carbon nanotubes (GNR@SWNT), was synthesized using confined polymerization and fusion of polycyclic aromatic hydrocarbon (PAH) molecules. Formation of the GNR is possible due to confinement effects provided by the one-dimensional space inside nanotubes, which helps to align coronene or perylene molecules edge to edge to achieve dimerization and oligomerization of the molecules into long nanoribbons. Almost 100% filling of SWNT with GNR is achieved while nanoribbon length is limited only by the length of the encapsulating nanotube. The PAH fusion reaction provides a very simple and easily scalable method to synthesize GNR@SWNT in macroscopic amounts. First-principle simulations indicate that encapsulation of the GNRs is energetically favorable and that the electronic structure of the encapsulated GNRs is the same as for the free-standing ones, pointing to possible applications of the GNR@SWNT structures in photonics and nanoelectronics.     

Cost modelling in underpinning projects

Large refurbishment projects are characterized by highly varied costs from one project to another. In Finnish underpinning, only retrospective analysis of costs has been available for the owner’s decision process. In order to develop tools for pre‐tender cost estimating and for comparison of different design solutions and evaluation of tenders of the underpinning project, two different cost models have been developed for research. In both models developed, the minimum data required is the pile length. In the more detailed model, the assessment is based on the design solution, including known pile types and the load transfer classification. Both models are easy to use, and the percentage of explained variance is fairly good in the more detailed model.     

Bioprotectives and probiotics for dry sausages

The microbial stability of dry sausages is determined by the combination and timing of different factors referred to as the hurdle-concept. However, the hurdles present in dry sausage are not sufficient to prevent the survival of Listeria monocytogenes or enterohemorrhagic Escherichia coli O157:H7. Recently bioprotective lactic acid bacteria, which in addition to the production of antimicrobial lactic acid, have been found to contribute to the safety of the dry sausage by producing antimicrobial peptide, i.e. bacteriocins and other low-molecular-mass compounds. Furthermore, the possibilities to use probotics in dry sausage manufacturing process has been addressed recently. As one possible mode of action for probiotics is the production of antimicrobial compounds, lactic acid bacteria may act as both probiotic and bioprotective culture as well as fermenting agent in meat product, such as dry sausage.     

Virtual reality in posturography.

Balance dysfunctions are common, especially among elderly people. Present methods for the diagnosis and evaluation of severity of dysfuntion have limited value. We present a system that makes it easy to implement different visual and mechanical perturbations for clinical investigations of balance and visual-vestibular interaction. The system combines virtual reality visual stimulation with force platform posturography on a moving platform. We evaluate our contruction's utility in a classification task between 33 healthy controls and 77 patients with Ménière's disease, using a series of tests with different visual and mechanical stimuli. Responses of patients and controls differ significantly in parameters computed from stabilograms. We also show that the series of tests achieves a classification accuracy slightly over 80% between controls and patients.     

Regulation of IRF and STAT gene expression by retinoic acid

Ex vivo production of cytokines as determined by whole blood stimulation and supernatant ELISA is partly determined by heritability. To assess the ability of this system to distinguish between high and low producers the laboratory error and individual variation were investigated. Whole blood samples from healthy volunteers were collected using endotoxin-free tubes and were incubated with 0 to 1000 ng/ml lipopolysaccharide concentrations for 4 and 24 h, and subsequently centrifuged. In the supernatants, TNF-alpha and IL10 were measured by ELISA. Coefficients of variation for the day-to-day variation in the blood sampling, transport and stimulation as well as in the whole blood stimulation per se ranged from 7.5% to 12.3%. The intra-individual variation was 15% (TNF-alpha) and 19% (IL10) in contrast to the inter-individual variation of, on average, 35%. No interchanging of ranks between high and low producers was observed after repeating the whole blood stimulation on distinct days. The whole blood stimulation system is able to distinguish high and low producers of TNF-alpha and IL10.