Model-driven design for the visual analysis of heterogeneous data

As heterogeneous data from different sources are being increasingly linked, it becomes difficult for users to understand how the data are connected, to identify what means are suitable to analyze a given data set, or to find out how to proceed for a given analysis task. We target this challenge with a new model-driven design process that effectively codesigns aspects of data, view, analytics, and tasks. We achieve this by using the workflow of the analysis task as a trajectory through data, interactive views, and analytical processes. The benefits for the analysis session go well beyond the pure selection of appropriate data sets and range from providing orientation or even guidance along a preferred analysis path to a potential overall speedup, allowing data to be fetched ahead of time. We illustrate the design process for a biomedical use case that aims at determining a treatment plan for cancer patients from the visual analysis of a large, heterogeneous clinical data pool. As an example for how to apply the comprehensive design approach, we present Stack'n'flip, a sample implementation which tightly integrates visualizations of the actual data with a map of available data sets, views, and tasks, thus capturing and communicating the analytical workflow through the required data sets.     

Energy-Efficient Thermal-Aware Autonomic Management of Virtualized HPC Cloud Infrastructure

Virtualized datacenters and clouds are being increasingly considered for traditional High-Performance Computing (HPC) workloads that have typically targeted Grids and conventional HPC platforms. However, maximizing energy efficiency and utilization of datacenter resources, and minimizing undesired thermal behavior while ensuring application performance and other Quality of Service (QoS) guarantees for HPC applications requires careful consideration of important and extremely challenging tradeoffs. Virtual Machine (VM) migration is one of the most common techniques used to alleviate thermal anomalies (i.e., hotspots) in cloud datacenter servers as it reduces load and, hence, the server utilization. In this article, the benefits of using other techniques such as voltage scaling and pinning (traditionally used for reducing energy consumption) for thermal management over VM migrations are studied in detail. As no single technique is the most efficient to meet temperature/performance optimization goals in all situations, an autonomic approach that performs energy-efficient thermal management while ensuring the QoS delivered to the users is proposed. To address the problem of VM allocation that arises during VM migrations, an innovative application-centric energy-aware strategy for Virtual Machine (VM) allocation is proposed. The proposed strategy ensures high resource utilization and energy efficiency through VM consolidation while satisfying application QoS by exploiting knowledge obtained through application profiling along multiple dimensions (CPU, memory, and network bandwidth utilization). To support our arguments, we present the results obtained from an experimental evaluation on real hardware using HPC workloads under different scenarios.     

Modeling of submicrometer gate GaAs field effect transistors

Before describing the mainFet modelings today available, the main technological evolutions ofMesfet andTegfet are summarized. It is brought some information on the various physical effects that occur in the devices and that must be taken into account in the models. It is shown that the different kinds of modelings (Monte Carlo, two dimensional, one dimensional) constitute a continuous chain, where the different elements appear strictly complementary. Finally, the present situation concerning modeling ofMesfet andTegfet will be presented.     

Integration of diskless workstations in unix united

This document evaluates the feasibility of diskless UNIX systems connected to a disk-providing machine via a local area network. The diskless UNIX systems are to be used as workstations in a UNIX United

1 UNIX is a trademark of A. T. & T. Bell Laboratories.

environment. Several solutions are presented and estimated to enable booting, file system access and swapping. Implementation techniques, compatible with the UNIX United philosophy, are proposed. Specific topics covered are file servers, swap servers, disk servers, indirect drivers, system call service access from kernel coroutines of UNIX processes, and communication subsystems. It is shown that the modifications to the UNIX system can be limited to one new device driver in the diskless workstation and one in the system providing the secondary storage facility.     

Hyperhomocysteinemia and Cardiovascular Disease: Is the Adenosinergic System the Missing Link?

The influence of hyperhomocysteinemia (HHCy) on cardiovascular disease (CVD) remains unclear. HHCy is associated with inflammation and atherosclerosis, and it is an independent risk factor for CVD, stroke and myocardial infarction. However, homocysteine (HCy)-lowering therapy does not affect the inflammatory state of CVD patients, and it has little influence on cardiovascular risk. The HCy degradation product hydrogen sulfide (H₂S) is a cardioprotector. Previous research proposed a positive role of H₂S in the cardiovascular system, and we discuss some recent data suggesting that HHCy worsens CVD by increasing the production of H₂S, which decreases the expression of adenosine A_2A receptors on the surface of immune and cardiovascular cells to cause inflammation and ischemia, respectively.     

The GNAQ T96S Mutation Affects Cell Signaling and Enhances the Oncogenic Properties of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC), the most common malignant tumor in the liver, grows and metastasizes rapidly. Despite advances in treatment modalities, the five-year survival rate of HCC remains less than 30%. We sought genetic mutations that may affect the oncogenic properties of HCC, using The Cancer Genome Atlas (TCGA) data analysis. We found that the GNAQ T96S mutation (threonine 96 to serine alteration of the Gαq protein) was present in 12 out of 373 HCC patients (3.2%). To examine the effect of the GNAQ T96S mutation on HCC, we transfected the SK-Hep-1 cell line with the wild-type or the mutant GNAQ T96S expression vector. Transfection with the wild-type GNAQ expression vector enhanced anchorage-independent growth, migration, and the MAPK pathways in the SK-Hep-1 cells compared to control vector transfection. Moreover, cell proliferation, anchorage-independent growth, migration, and the MAPK pathways were further enhanced in the SK-Hep-1 cells transfected with the GNAQ T96S expression vector compared to the wild-type GNAQ-transfected cells. In silico structural analysis shows that the substitution of the GNAQ amino acid threonine 96 with a serine may destabilize the interaction between the regulator of G protein signaling (RGS) protein and GNAQ. This may reduce the inhibitory effect of RGS on GNAQ signaling, enhancing the GNAQ signaling pathway. Single nucleotide polymorphism (SNP) genotyping analysis for Korean HCC patients shows that the GNAQ T96S mutation was found in only one of the 456 patients (0.22%). Our data suggest that the GNAQ T96S hotspot mutation may play an oncogenic role in HCC by potentiating the GNAQ signal transduction pathway.     

The Multifunctional Sactipeptide Ruminococcin C1 Displays Potent Antibacterial Activity In Vivo as Well as Other Beneficial Properties for Human Health

The world is on the verge of a major antibiotic crisis as the emergence of resistant bacteria is increasing, and very few novel molecules have been discovered since the 1960s. In this context, scientists have been exploring alternatives to conventional antibiotics, such as ribosomally synthesized and post-translationally modified peptides (RiPPs). Interestingly, the highly potent in vitro antibacterial activity and safety of ruminococcin C1, a recently discovered RiPP belonging to the sactipeptide subclass, has been demonstrated. The present results show that ruminococcin C1 is efficient at curing infection and at protecting challenged mice from Clostridium perfringens with a lower dose than the conventional antibiotic vancomycin. Moreover, antimicrobial peptide (AMP) is also effective against this pathogen in the complex microbial community of the gut environment, with a selective impact on a few bacterial genera, while maintaining a global homeostasis of the microbiome. In addition, ruminococcin C1 exhibits other biological activities that could be beneficial for human health, as well as other fields of applications. Overall, this study, by using an in vivo infection approach, confirms the antimicrobial clinical potential and highlights the multiple functional properties of ruminococcin C1, thus extending its therapeutic interest.     

The Importance of Free Fatty Chain Length on the Lipid Organization in the Long Periodicity Phase

The skin’s barrier ability is an essential function for terrestrial survival, which is controlled by intercellular lipids within the stratum corneum (SC) layer. In this barrier, free fatty acids (FFAs) are an important lipid class. As seen in inflammatory skin diseases, when the lipid chain length is reduced, a reduction in the barrier’s performance is observed. In this study, we have investigated the contributing effects of various FFA chain lengths on the lamellar phase, lateral packing. The repeat distance of the lamellar phase increased with FFA chain length (C20–C28), while shorter FFAs (C16 to C18) had the opposite behaviour. While the lateral packing was affected, the orthorhombic to hexagonal to fluid phase transitions were not affected by the FFA chain length. Porcine SC lipid composition mimicking model was then used to investigate the proportional effect of shorter FFA C16, up to 50% content of the total FFA mixture. At this level, no difference in the overall lamellar phases and lateral packing was observed, while a significant increase in the water permeability was detected. Our results demonstrate a FFA C16 threshold that must be exceeded before the structure and barrier function of the long periodicity phase (LPP) is affected. These results are important to understand the lipid behaviour in this unique LPP structure as well as for the understanding, treatment, and development of inflammatory skin conditions.     

Quantification of secondary structure prediction improvement using multiple alignments

The use of multiple sequence alignments for secondary structurepredictions is analysed. Seven different protein families, containingonly sequences of known structure, were considered to providea range of alignment and prediction conditions. Using alignmentsobtained by spatial superposition of main chain atoms in knowntertiary protein structures allowed a mean of 8% in secondarystructure prediction accuracy, when compared to those obtainedfrom the individual sequences. Substitution of these alignmentsby those determined directly from an automated sequence alignmentalgorithm showed variations in the prediction accuracy whichcorrelated with the quality of the multiple alignments and distanceof the primary sequence. Secondary structure predictions canbe reliably improved using alignments from an automatic alignmentprocedure with a mean increase of 6.87percnt;, giving an overallprediction accuracy of 68.5%, if there is a minimum of 25% sequenceidentity between all sequences in a family.